seqret



Wiki

   The master copies of EMBOSS documentation are available at
   http://emboss.open-bio.org/wiki/Appdocs on the EMBOSS Wiki.

   Please help by correcting and extending the Wiki pages.

Function

   Read and write (return) sequences

Description

   seqret reads in one or more sequences and writes them out again. The
   sequence input may be a literal sequence or read from a database, file,
   file of sequence names, or even the command-line or the output of
   another programs. The sequence output can be written to screen, to
   file, or passed to another program. A wide range of standard sequence
   formats may be specified for input and output. If you don't specify the
   input format, seqret will try a set of possible formats until it reads
   it in successfully. The sequence input and output, as for all EMBOSS
   programs, is described by a Uniform Sequence Address. This is is a very
   flexible way of specifying one or more sequences from a variety of
   sources and includes sequence files, database queries and external
   applications.

   There are many options built-in into EMBOSS for detailed specification
   of the input and output sequences, for example the sequence type, file
   format. specification of sequence regions by begin and end positions,
   or generation of the reverse complement of a nucleic acid sequence. On
   output seqret can change the case of the sequence to upper or to lower
   case.

   seqret is useful for a variety of tasks, including extracting sequences
   from databases, displaying sequences, reformatting sequences, producing
   the reverse complement of a sequence, extracting fragments of a
   sequence, sequence case conversion or any combination of the above
   functions.

Usage

   Here is a sample session with seqret

   Extract an entry from a database and write it to a file:


% seqret
Read and write (return) sequences
Input (gapped) sequence(s): tembl:x65923
output sequence(s) [x65923.fasta]:


   Go to the input files for this example
   Go to the output files for this example

   Example 2

   Read all entries in the database 'tembl' that start with 'ab' and write
   them to a file. In this example the specification is all done in the
   command line and to stop Unix getting confused by the '*' character, it
   has to have a backslash ('\') before it:


% seqret "tembl:ab*"  aball.seq
Read and write (return) sequences


   Go to the output files for this example

   Example 3

   seqret does not read in features by default because this results in
   slightly faster performance. If however you wish to read in features
   with your sequence and write them out on output, using '-feature' will
   change the default behaviour to use any features present in the
   sequence. N.B. use embl format for the output file as the default
   format 'fasta' reports the features in gff (file "<seqname>.gff")


% seqret -feature
Read and write (return) sequences
Input (gapped) sequence(s): tembl:x65923
output sequence(s) [x65923.fasta]: embl::x65923.embl


   Go to the output files for this example

   Example 4

   Display the contents of the sequence on the screen:


% seqret
Read and write (return) sequences
Input (gapped) sequence(s): tembl:x65923
output sequence(s) [x65923.fasta]: stdout

>X65923 X65923.1 H.sapiens fau mRNA
ttcctctttctcgactccatcttcgcggtagctgggaccgccgttcagtcgccaatatgc
agctctttgtccgcgcccaggagctacacaccttcgaggtgaccggccaggaaacggtcg
cccagatcaaggctcatgtagcctcactggagggcattgccccggaagatcaagtcgtgc
tcctggcaggcgcgcccctggaggatgaggccactctgggccagtgcggggtggaggccc
tgactaccctggaagtagcaggccgcatgcttggaggtaaagttcatggttccctggccc
gtgctggaaaagtgagaggtcagactcctaaggtggccaaacaggagaagaagaagaaga
agacaggtcgggctaagcggcggatgcagtacaaccggcgctttgtcaacgttgtgccca
cctttggcaagaagaagggccccaatgccaactcttaagtcttttgtaattctggctttc
tctaataaaaaagccacttagttcagtcaaaaaaaaaa


   Example 5

   Write the result in GCG format by using the qualifier '-osformat'.


% seqret -osf gcg
Read and write (return) sequences
Input (gapped) sequence(s): tembl:x65923
output sequence(s) [x65923.gcg]:


   Go to the output files for this example

   Example 6

   Write the result in GCG format by specifying the format in the output
   USA on the command line.


% seqret -outseq gcg::x65923.gcg
Read and write (return) sequences
Input (gapped) sequence(s): tembl:x65923


   Example 7

   Write the result in GCG format by specifying the format in the output
   USA at the prompt.


% seqret
Read and write (return) sequences
Input (gapped) sequence(s): tembl:x65923
output sequence(s) [x65923.fasta]: gcg::x65923.gcg


   Example 8

   Write the reverse-complement of a sequence:


% seqret -srev
Read and write (return) sequences
Input (gapped) sequence(s): tembl:x65923
output sequence(s) [x65923.fasta]:


   Go to the output files for this example

   Example 9

   Extract the bases between the positions starting at 5 and ending at 25:


% seqret -sbegin 5 -send 25
Read and write (return) sequences
Input (gapped) sequence(s): tembl:x65923
output sequence(s) [x65923.fasta]:


   Go to the output files for this example

   Example 10

   Extract the bases between the positions starting at 5 and ending at 5
   bases before the end of the sequence:


% seqret -sbegin 5 -send -5
Read and write (return) sequences
Input (gapped) sequence(s): tembl:x65923
output sequence(s) [x65923.fasta]:


   Go to the output files for this example

   Example 11

   Read all entries in the database 'tembl' that start with 'h' and write
   them to a file:


% seqret
Read and write (return) sequences
Input (gapped) sequence(s): tembl:h*
output sequence(s) [h45989.fasta]: hall.seq


   Go to the output files for this example

Command line arguments

Read and write (return) sequences
Version: EMBOSS:6.6.0.0

   Standard (Mandatory) qualifiers:
  [-sequence]          seqall     (Gapped) sequence(s) filename and optional
                                  format, or reference (input USA)
  [-outseq]            seqoutall  [.] Sequence set(s)
                                  filename and optional format (output USA)

   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers:
   -feature            boolean    Use feature information
   -firstonly          boolean    [N] Read one sequence and stop

   Associated qualifiers:

   "-sequence" associated qualifiers
   -sbegin1            integer    Start of each sequence to be used
   -send1              integer    End of each sequence to be used
   -sreverse1          boolean    Reverse (if DNA)
   -sask1              boolean    Ask for begin/end/reverse
   -snucleotide1       boolean    Sequence is nucleotide
   -sprotein1          boolean    Sequence is protein
   -slower1            boolean    Make lower case
   -supper1            boolean    Make upper case
   -scircular1         boolean    Sequence is circular
   -squick1            boolean    Read id and sequence only
   -sformat1           string     Input sequence format
   -iquery1            string     Input query fields or ID list
   -ioffset1           integer    Input start position offset
   -sdbname1           string     Database name
   -sid1               string     Entryname
   -ufo1               string     UFO features
   -fformat1           string     Features format
   -fopenfile1         string     Features file name

   "-outseq" associated qualifiers
   -osformat2          string     Output seq format
   -osextension2       string     File name extension
   -osname2            string     Base file name
   -osdirectory2       string     Output directory
   -osdbname2          string     Database name to add
   -ossingle2          boolean    Separate file for each entry
   -oufo2              string     UFO features
   -offormat2          string     Features format
   -ofname2            string     Features file name
   -ofdirectory2       string     Output directory

   General qualifiers:
   -auto               boolean    Turn off prompts
   -stdout             boolean    Write first file to standard output
   -filter             boolean    Read first file from standard input, write
                                  first file to standard output
   -options            boolean    Prompt for standard and additional values
   -debug              boolean    Write debug output to program.dbg
   -verbose            boolean    Report some/full command line options
   -help               boolean    Report command line options and exit. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose
   -warning            boolean    Report warnings
   -error              boolean    Report errors
   -fatal              boolean    Report fatal errors
   -die                boolean    Report dying program messages
   -version            boolean    Report version number and exit


Input file format

   seqret reads one or more nucleotide or protein sequences.

   The input is a standard EMBOSS sequence query (also known as a 'USA').

   Major sequence database sources defined as standard in EMBOSS
   installations include srs:embl, srs:uniprot and ensembl

   Data can also be read from sequence output in any supported format
   written by an EMBOSS or third-party application.

   The input format can be specified by using the command-line qualifier
   -sformat xxx, where 'xxx' is replaced by the name of the required
   format. The available format names are: gff (gff3), gff2, embl (em),
   genbank (gb, refseq), ddbj, refseqp, pir (nbrf), swissprot (swiss, sw),
   dasgff and debug.

   See: http://emboss.sf.net/docs/themes/SequenceFormats.html for further
   information on sequence formats.

  Input files for usage example

   'tembl:x65923' is a sequence entry in the example nucleic acid database
   'tembl'

  Database entry: tembl:x65923

ID   X65923; SV 1; linear; mRNA; STD; HUM; 518 BP.
XX
AC   X65923;
XX
DT   13-MAY-1992 (Rel. 31, Created)
DT   18-APR-2005 (Rel. 83, Last updated, Version 11)
XX
DE   H.sapiens fau mRNA
XX
KW   fau gene.
XX
OS   Homo sapiens (human)
OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC   Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae;
OC   Homo.
XX
RN   [1]
RP   1-518
RA   Michiels L.M.R.;
RT   ;
RL   Submitted (29-APR-1992) to the INSDC.
RL   L.M.R. Michiels, University of Antwerp, Dept of Biochemistry,
RL   Universiteisplein 1, 2610 Wilrijk, BELGIUM
XX
RN   [2]
RP   1-518
RX   PUBMED; 8395683.
RA   Michiels L., Van der Rauwelaert E., Van Hasselt F., Kas K., Merregaert J.;
RT   "fau cDNA encodes a ubiquitin-like-S30 fusion protein and is expressed as
RT   an antisense sequence in the Finkel-Biskis-Reilly murine sarcoma virus";
RL   Oncogene 8(9):2537-2546(1993).
XX
DR   Ensembl-Gn; ENSG00000149806; Homo_sapiens.
DR   Ensembl-Tr; ENST00000279259; Homo_sapiens.
DR   Ensembl-Tr; ENST00000434372; Homo_sapiens.
DR   Ensembl-Tr; ENST00000525297; Homo_sapiens.
DR   Ensembl-Tr; ENST00000526555; Homo_sapiens.
DR   Ensembl-Tr; ENST00000527548; Homo_sapiens.
DR   Ensembl-Tr; ENST00000529259; Homo_sapiens.
DR   Ensembl-Tr; ENST00000529639; Homo_sapiens.
DR   Ensembl-Tr; ENST00000531743; Homo_sapiens.
XX
FH   Key             Location/Qualifiers
FH
FT   source          1..518
FT                   /organism="Homo sapiens"
FT                   /chromosome="11q"
FT                   /map="13"
FT                   /mol_type="mRNA"
FT                   /clone_lib="cDNA"
FT                   /clone="pUIA 631"
FT                   /tissue_type="placenta"
FT                   /db_xref="taxon:9606"
FT   misc_feature    57..278
FT                   /note="ubiquitin like part"
FT   CDS             57..458
FT                   /gene="fau"
FT                   /db_xref="GDB:135476"
FT                   /db_xref="GOA:P35544"
FT                   /db_xref="GOA:P62861"
FT                   /db_xref="H-InvDB:HIT000322806.14"
FT                   /db_xref="HGNC:3597"
FT                   /db_xref="InterPro:IPR000626"
FT                   /db_xref="InterPro:IPR006846"
FT                   /db_xref="InterPro:IPR019954"
FT                   /db_xref="InterPro:IPR019955"
FT                   /db_xref="InterPro:IPR019956"
FT                   /db_xref="PDB:2L7R"
FT                   /db_xref="UniProtKB/Swiss-Prot:P35544"
FT                   /db_xref="UniProtKB/Swiss-Prot:P62861"
FT                   /protein_id="CAA46716.1"
FT                   /translation="MQLFVRAQELHTFEVTGQETVAQIKAHVASLEGIAPEDQVVLLAG
FT                   APLEDEATLGQCGVEALTTLEVAGRMLGGKVHGSLARAGKVRGQTPKVAKQEKKKKKTG
FT                   RAKRRMQYNRRFVNVVPTFGKKKGPNANS"
FT   misc_feature    98..102
FT                   /note="nucleolar localization signal"
FT   misc_feature    279..458
FT                   /note="S30 part"
FT   polyA_signal    484..489
FT   polyA_site      509
XX
SQ   Sequence 518 BP; 125 A; 139 C; 148 G; 106 T; 0 other;
     ttcctctttc tcgactccat cttcgcggta gctgggaccg ccgttcagtc gccaatatgc        60
     agctctttgt ccgcgcccag gagctacaca ccttcgaggt gaccggccag gaaacggtcg       120
     cccagatcaa ggctcatgta gcctcactgg agggcattgc cccggaagat caagtcgtgc       180
     tcctggcagg cgcgcccctg gaggatgagg ccactctggg ccagtgcggg gtggaggccc       240
     tgactaccct ggaagtagca ggccgcatgc ttggaggtaa agttcatggt tccctggccc       300
     gtgctggaaa agtgagaggt cagactccta aggtggccaa acaggagaag aagaagaaga       360
     agacaggtcg ggctaagcgg cggatgcagt acaaccggcg ctttgtcaac gttgtgccca       420
     cctttggcaa gaagaagggc cccaatgcca actcttaagt cttttgtaat tctggctttc       480
     tctaataaaa aagccactta gttcagtcaa aaaaaaaa                               518
//

Output file format

   The output is a standard EMBOSS sequence file.

   The results can be output in one of several styles by using the
   command-line qualifier -osformat xxx, where 'xxx' is replaced by the
   name of the required format. The available format names are: embl,
   genbank, gff, pir, swiss, dasgff, debug, listfile, dbmotif, diffseq,
   excel, feattable, motif, nametable, regions, seqtable, simple, srs,
   table, tagseq.

   See: http://emboss.sf.net/docs/themes/SequenceFormats.html for further
   information on sequence formats.

   The output from seqret is one or more sequences, and by default will be
   written in FASTA format.

   If the '-firstonly' qualifier is used then only the first sequence of
   the input USA specification will be written out.

   In some cases the output filename will be the same as the input
   filename, but as seqret reads only the first sequence before opening
   the output file it may try to overwrite the input. Note that this is
   not true of seqretset which reads all sequences into memory at startup,
   but which can need a large amount of memory for many sequences.

  Output files for usage example

  File: x65923.fasta

>X65923 X65923.1 H.sapiens fau mRNA
ttcctctttctcgactccatcttcgcggtagctgggaccgccgttcagtcgccaatatgc
agctctttgtccgcgcccaggagctacacaccttcgaggtgaccggccaggaaacggtcg
cccagatcaaggctcatgtagcctcactggagggcattgccccggaagatcaagtcgtgc
tcctggcaggcgcgcccctggaggatgaggccactctgggccagtgcggggtggaggccc
tgactaccctggaagtagcaggccgcatgcttggaggtaaagttcatggttccctggccc
gtgctggaaaagtgagaggtcagactcctaaggtggccaaacaggagaagaagaagaaga
agacaggtcgggctaagcggcggatgcagtacaaccggcgctttgtcaacgttgtgccca
cctttggcaagaagaagggccccaatgccaactcttaagtcttttgtaattctggctttc
tctaataaaaaagccacttagttcagtcaaaaaaaaaa

  Output files for usage example 2

  File: aball.seq

>AB009602 AB009602.1 Schizosaccharomyces pombe mRNA for MET1 homolog, partial cd
s.
gttcgatgcctaaaataccttcttttgtccctacacagaccacagttttcctaatggctt
tacaccgactagaaattcttgtgcaagcactaattgaaagcggttggcctagagtgttac
cggtttgtatagctgagcgcgtctcttgccctgatcaaaggttcattttctctactttgg
aagacgttgtggaagaatacaacaagtacgagtctctcccccctggtttgctgattactg
gatacagttgtaatacccttcgcaacaccgcgtaactatctatatgaattattttccctt
tattatatgtagtaggttcgtctttaatcttcctttagcaagtcttttactgttttcgac
ctcaatgttcatgttcttaggttgttttggataatatgcggtcagtttaatcttcgttgt
ttcttcttaaaatatttattcatggtttaatttttggtttgtacttgttcaggggccagt
tcattatttactctgtttgtatacagcagttcttttatttttagtatgattttaatttaa
aacaattctaatggtcaaaaa
>AB000095 AB000095.1 Homo sapiens mRNA for hepatocyte growth factor activator in
hibitor, complete cds.
cggccgagcccagctctccgagcaccgggtcggaagccgcgacccgagccgcgcaggaag
ctgggaccggaacctcggcggacccggccccacccaactcacctgcgcaggtcaccagca
ccctcggaacccagaggcccgcgctctgaaggtgacccccctggggaggaaggcgatggc
ccctgcgaggacgatggcccgcgcccgcctcgccccggccggcatccctgccgtcgcctt
gtggcttctgtgcacgctcggcctccagggcacccaggccgggccaccgcccgcgccccc
tgggctgcccgcgggagccgactgcctgaacagctttaccgccggggtgcctggcttcgt
gctggacaccaacgcctcggtcagcaacggagctaccttcctggagtcccccaccgtgcg
ccggggctgggactgcgtgcgcgcctgctgcaccacccagaactgcaacttggcgctagt
ggagctgcagcccgaccgcggggaggacgccatcgccgcctgcttcctcatcaactgcct
ctacgagcagaacttcgtgtgcaagttcgcgcccagggagggcttcatcaactacctcac
gagggaagtgtaccgctcctaccgccagctgcggacccagggctttggagggtctgggat
ccccaaggcctgggcaggcatagacttgaaggtacaaccccaggaacccctggtgctgaa
ggatgtggaaaacacagattggcgcctactgcggggtgacacggatgtcagggtagagag
gaaagacccaaaccaggtggaactgtggggactcaaggaaggcacctacctgttccagct
gacagtgactagctcagaccacccagaggacacggccaacgtcacagtcactgtgctgtc
caccaagcagacagaagactactgcctcgcatccaacaaggtgggtcgctgccggggctc
tttcccacgctggtactatgaccccacggagcagatctgcaagagtttcgtttatggagg
ctgcttgggcaacaagaacaactaccttcgggaagaagagtgcattctagcctgtcgggg
tgtgcaaggcccctccatggaaaggcgccatccagtgtgctctggcacctgtcagcccac
ccagttccgctgcagcaatggctgctgcatcgacagtttcctggagtgtgacgacacccc
caactgccccgacgcctccgacgaggctgcctgtgaaaaatacacgagtggctttgacga
gctccagcgcatccatttccccagtgacaaagggcactgcgtggacctgccagacacagg
actctgcaaggagagcatcccgcgctggtactacaaccccttcagcgaacactgcgcccg
ctttacctatggtggttgttatggcaacaagaacaactttgaggaagagcagcagtgcct
cgagtcttgtcgcggcatctccaagaaggatgtgtttggcctgaggcgggaaatccccat
tcccagcacaggctctgtggagatggctgtcgcagtgttcctggtcatctgcattgtggt
ggtggtagccatcttgggttactgcttcttcaagaaccagagaaaggacttccacggaca
ccaccaccacccaccacccacccctgccagctccactgtctccactaccgaggacacgga
gcacctggtctataaccacaccacccggcccctctgagcctgggtctcaccggctctcac
ctggccctgcttcctgcttgccaaggcagaggcctgggctgggaaaaactttggaaccag
actcttgcctgtttcccaggcccactgtgcctcagagaccagggctccagcccctcttgg
agaagtctcagctaagctcacgtcctgagaaagctcaaaggtttggaaggagcagaaaac
ccttgggccagaagtaccagactagatggacctgcctgcataggagtttggaggaagttg
gagttttgtttcctctgttcaaagctgcctgtccctaccccatggtgctaggaagaggag
tggggtggtgtcagaccctggaggccccaaccctgtcctcccgagctcctcttccatgct
gtgcgcccagggctgggaggaaggacttccctgtgtagtttgtgctgtaaagagttgctt
tttgtttatttaatgctgtggcatgggtgaagaggaggggaagaggcctgtttggcctct
ctgtcctctcttcctcttcccccaagattgagctctctgcccttgatcagccccaccctg


  [Part of this file has been deleted for brevity]

ccttgtcaggcggaagggcatcaacggcgggcttctcccgctgggcctgagcccgttgat
ctccccaagctgcaagcgaaccttgcgggtcaaggtcgagggcaatcacggattcccctg
cctctgtggccgcgacggcaatggcagcagcgagggtagtttttcccgcgccgcccttct
gcgtgaccagagcaattgtcttcatgcctgcactatagcattaaggcactaaagcgtcaa
agcgccatagcggcatagcggcatagcggcatagcgctaaaatgctatagcattattaaa
tacagcgctacagcgctataatgctgcaacggttaggaccgcaatttgcgccccgggccg
gttgcgctatcgaccagctcaattaactgctcgggctcggacgcgaaccacgcgaagctg
ccccaagccaaggagtcgagggagccacggttgatgagagctttgttgtaggtggaccag
ttggtgattttgaacttttgctttgccacggaacggtctgcgttgtcgggaagatgcgtg
atctgatccttcaactcagcaaaagttcgatttattcaacaaagccacgttgtgtctcaa
aatctctgatgttacattgcacaagataaaaatatatcatcatgaacaataaaactgtct
gcttacataaacagtaatacaaggggtgttatgagccatattcaacgggaaacgtcttgc
tcgaagccgcgattaaattccaacatggatgctgatttatatgggtataaatgggctcgc
gataatgtcgggcaatcaggtgcgacaatctatcgattgtatgggaagcccgatgcgcca
gagttgtttctgaaacatggcaaaggtagcgttgccaatgatgttacagatgagatggtc
agactaaactggctgacggaatttatgcctcttccgaccatcaagcattttatccgtact
cctgatgatgcatggttactcaccactgcgatccccgggaaaacagcattccaggtatta
gaagaatatcctgattcaggtgaaaatattgttgatgcgctggcagtgttcctgcgccgg
ttgcattcgattcctgtttgtaattgtccttttaacagcgatcgcgtatttcgtctcgct
caggcgcaatcacgaatgaataacggtttggttgatgcgagtgattttgatgacgagcgt
aatggctggcctgttgaacaagtctggaaagaaatgcataagcttttgccattctcaccg
gattcagtcgtcactcatggtgatttctcacttgataaccttatttttgacgaggggaaa
ttaataggttgtattgatgttggacgagtcggaatcgcagaccgataccaggatcttgcc
atcctatggaactgcctcggtgagttttctccttcattacagaaacggctttttcaaaaa
tatggtattgataatcctgatatgaataaattgcagtttcatttgatgctcgatgagttt
ttctaatcagaattggttaattggttgtaacactggcagagcattacgctgacttgacgg
gacggcggctttgttgaataaatcgcattcgccattcaggctgcgcaactgttgggaagg
gcgatcggtgcgggcctcttcgctattacgccagctggcgaaagggggatgtgctgcaag
gcgattaagttgggtaacgccagggttttcccagtcacgacgttgtaaaacgacggccag
tgccaagcttgcatgcctgcaggtcgactctagaggatccccgggtaccgagctcgaatt
cgtaatcatggtcatagctgtttcctgtgtgaaattgttatccgctcacaattccacaca
acatacgagccggaagcataaagtgtaaagcctggggtgcctaatgagtgagctaactca
cattaattgcgttgcgctcactgcccgctttccagtcgggaaacctgtcgtgccagctgc
attaatgaatcggccaacgcgcggggagaggcggtttgcgtattggcgaacttttgctga
gttgaaggatcagatcacgcatcttcccgacaacgcagaccgttccgtggcaaagcaaaa
gttcaaaatcagtaaccgtcagtgccgataagttcaaagttaaacctggtgttgatacca
acattgaaacgctgatcgaaaacgcgctgaaaaacgctgctgaatgtgcgagcttcttcc
gcttcctcgctcactgactcgctgcgctcggtcgttcggctgcggcgagcggtatcagct
cactcaaaggcggtaatacggttatccacagaatcaggggataacgcaggaaagaacatg
tgagcaaaaggccagcaaaaggccaggaaccgtaaaaaggccgcgttgctggcgtttttc
cataggctccgcccccctgacgagcatcacaaaaatcgacgctcaagtcagaggtggcga
aacccgacaggactataaagataccaggcgtttccccctggaagctccctcgtgcgctct
cctgttccgaccctgccgcttaccggatacctgtccgcctttctcccttcgggaagcgtg
gcgctttctcaatgctcacgctgtaggtatctcagttcggtgtaggtcgttcgctccaag
ctgggctgtgtgcacgaaccccccgttcagcccgaccgctgcgccttatccggtaactat
cgtcttgagtccaacccggtaagacacgacttatcgccactggcagcagccactggtaac
aggattagcagagcgaggtatgtaggcggtgctacagagttcttgaagtggtggcctaac
tacggctacactagaaggacagtatttggtatctgcgctctgctgaagccagttaccttc
ggaaaaagagttggtagctcttgatccggcaaacaaaccaccgctggtagcggtggtttt
tttgtttgcaagcagcagattacgcgcagaaaaaaaggatctcaagaagatcctttgatc
ttttctacggggtctgacgctcagtggaacgatccgtcga

  Output files for usage example 3

  File: x65923.embl

ID   X65923; SV 1; linear; mRNA; STD; HUM; 518 BP.
XX
AC   X65923;
XX
DT   13-MAY-1992 (Rel. 31, Created)
DT   18-APR-2005 (Rel. 83, Last updated, Version 11)
XX
DE   H.sapiens fau mRNA
XX
KW   fau gene.
XX
OS   Homo sapiens (human)
OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC   Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae;
OC   Homo.
XX
RN   [1]
RP   1-518
RA   Michiels L.M.R.;
RT   ;
RL   Submitted (29-APR-1992) to the INSDC.
RL   L.M.R. Michiels, University of Antwerp, Dept of Biochemistry,
RL   Universiteisplein 1, 2610 Wilrijk, BELGIUM.
XX
RN   [2]
RP   1-518
RX   PUBMED; 8395683.
RA   Michiels L., Van der Rauwelaert E., Van Hasselt F., Kas K., Merregaert J.;
RT   "fau cDNA encodes a ubiquitin-like-S30 fusion protein and is expressed as
RT   an antisense sequence in the Finkel-Biskis-Reilly murine sarcoma virus";
RL   Oncogene 8(9):2537-2546(1993).
XX
DR   Ensembl-Gn; ENSG00000149806; Homo_sapiens.
DR   Ensembl-Tr; ENST00000279259; Homo_sapiens.
DR   Ensembl-Tr; ENST00000434372; Homo_sapiens.
DR   Ensembl-Tr; ENST00000525297; Homo_sapiens.
DR   Ensembl-Tr; ENST00000526555; Homo_sapiens.
DR   Ensembl-Tr; ENST00000527548; Homo_sapiens.
DR   Ensembl-Tr; ENST00000529259; Homo_sapiens.
DR   Ensembl-Tr; ENST00000529639; Homo_sapiens.
DR   Ensembl-Tr; ENST00000531743; Homo_sapiens.
XX
FH   Key             Location/Qualifiers
FH
FT   source          1..518
FT                   /organism="Homo sapiens"
FT                   /chromosome="11q"
FT                   /map="13"
FT                   /mol_type="mRNA"
FT                   /clone_lib="cDNA"
FT                   /clone="pUIA 631"
FT                   /tissue_type="placenta"
FT                   /db_xref="taxon:9606"
FT   misc_feature    57..278
FT                   /note="ubiquitin like part"
FT   CDS             57..458
FT                   /gene="fau"
FT                   /db_xref="GDB:135476"
FT                   /db_xref="GOA:P35544"
FT                   /db_xref="GOA:P62861"
FT                   /db_xref="H-InvDB:HIT000322806.14"
FT                   /db_xref="HGNC:3597"
FT                   /db_xref="InterPro:IPR000626"
FT                   /db_xref="InterPro:IPR006846"
FT                   /db_xref="InterPro:IPR019954"
FT                   /db_xref="InterPro:IPR019955"
FT                   /db_xref="InterPro:IPR019956"
FT                   /db_xref="PDB:2L7R"
FT                   /db_xref="UniProtKB/Swiss-Prot:P35544"
FT                   /db_xref="UniProtKB/Swiss-Prot:P62861"
FT                   /protein_id="CAA46716.1"
FT                   /translation="MQLFVRAQELHTFEVTGQETVAQIKAHVASLEGIAPEDQVVLLAG
FT                   APLEDEATLGQCGVEALTTLEVAGRMLGGKVHGSLARAGKVRGQTPKVAKQEKKKKKTG
FT                   RAKRRMQYNRRFVNVVPTFGKKKGPNANS"
FT   misc_feature    98..102
FT                   /note="nucleolar localization signal"
FT   misc_feature    279..458
FT                   /note="S30 part"
FT   polyA_signal    484..489
FT   polyA_site      509
XX
SQ   Sequence 518 BP; 125 A; 139 C; 148 G; 106 T; 0 other;
     ttcctctttc tcgactccat cttcgcggta gctgggaccg ccgttcagtc gccaatatgc        60
     agctctttgt ccgcgcccag gagctacaca ccttcgaggt gaccggccag gaaacggtcg       120
     cccagatcaa ggctcatgta gcctcactgg agggcattgc cccggaagat caagtcgtgc       180
     tcctggcagg cgcgcccctg gaggatgagg ccactctggg ccagtgcggg gtggaggccc       240
     tgactaccct ggaagtagca ggccgcatgc ttggaggtaa agttcatggt tccctggccc       300
     gtgctggaaa agtgagaggt cagactccta aggtggccaa acaggagaag aagaagaaga       360
     agacaggtcg ggctaagcgg cggatgcagt acaaccggcg ctttgtcaac gttgtgccca       420
     cctttggcaa gaagaagggc cccaatgcca actcttaagt cttttgtaat tctggctttc       480
     tctaataaaa aagccactta gttcagtcaa aaaaaaaa                               518
//

  Output files for usage example 5

  File: x65923.gcg

!!NA_SEQUENCE 1.0

H.sapiens fau mRNA

X65923  Length: 518  Type: N  Check: 2981 ..

   1 ttcctctttc tcgactccat cttcgcggta gctgggaccg ccgttcagtc

  51 gccaatatgc agctctttgt ccgcgcccag gagctacaca ccttcgaggt

 101 gaccggccag gaaacggtcg cccagatcaa ggctcatgta gcctcactgg

 151 agggcattgc cccggaagat caagtcgtgc tcctggcagg cgcgcccctg

 201 gaggatgagg ccactctggg ccagtgcggg gtggaggccc tgactaccct

 251 ggaagtagca ggccgcatgc ttggaggtaa agttcatggt tccctggccc

 301 gtgctggaaa agtgagaggt cagactccta aggtggccaa acaggagaag

 351 aagaagaaga agacaggtcg ggctaagcgg cggatgcagt acaaccggcg

 401 ctttgtcaac gttgtgccca cctttggcaa gaagaagggc cccaatgcca

 451 actcttaagt cttttgtaat tctggctttc tctaataaaa aagccactta

 501 gttcagtcaa aaaaaaaa


  Output files for usage example 8

  File: x65923.fasta

>X65923 X65923.1 H.sapiens fau mRNA
ttttttttttgactgaactaagtggcttttttattagagaaagccagaattacaaaagac
ttaagagttggcattggggcccttcttcttgccaaaggtgggcacaacgttgacaaagcg
ccggttgtactgcatccgccgcttagcccgacctgtcttcttcttcttcttctcctgttt
ggccaccttaggagtctgacctctcacttttccagcacgggccagggaaccatgaacttt
acctccaagcatgcggcctgctacttccagggtagtcagggcctccaccccgcactggcc
cagagtggcctcatcctccaggggcgcgcctgccaggagcacgacttgatcttccggggc
aatgccctccagtgaggctacatgagccttgatctgggcgaccgtttcctggccggtcac
ctcgaaggtgtgtagctcctgggcgcggacaaagagctgcatattggcgactgaacggcg
gtcccagctaccgcgaagatggagtcgagaaagaggaa

  Output files for usage example 9

  File: x65923.fasta

>X65923 X65923.1 H.sapiens fau mRNA
tctttctcgactccatcttcg

  Output files for usage example 10

  File: x65923.fasta

>X65923 X65923.1 H.sapiens fau mRNA
tctttctcgactccatcttcgcggtagctgggaccgccgttcagtcgccaatatgcagct
ctttgtccgcgcccaggagctacacaccttcgaggtgaccggccaggaaacggtcgccca
gatcaaggctcatgtagcctcactggagggcattgccccggaagatcaagtcgtgctcct
ggcaggcgcgcccctggaggatgaggccactctgggccagtgcggggtggaggccctgac
taccctggaagtagcaggccgcatgcttggaggtaaagttcatggttccctggcccgtgc
tggaaaagtgagaggtcagactcctaaggtggccaaacaggagaagaagaagaagaagac
aggtcgggctaagcggcggatgcagtacaaccggcgctttgtcaacgttgtgcccacctt
tggcaagaagaagggccccaatgccaactcttaagtcttttgtaattctggctttctcta
ataaaaaagccacttagttcagtcaaaaaa

  Output files for usage example 11

  File: hall.seq

>H45989 H45989.1 yo13c02.s1 Soares adult brain N2b5HB55Y Homo sapiens cDNA clone
 IMAGE:177794 3', mRNA sequence.
ccggnaagctcancttggaccaccgactctcgantgnntcgccgcgggagccggntggan
aacctgagcgggactggnagaaggagcagagggaggcagcacccggcgtgacggnagtgt
gtggggcactcaggccttccgcagtgtcatctgccacacggaaggcacggccacgggcag
gggggtctatgatcttctgcatgcccagctggcatggccccacgtagagtggnntggcgt
ctcggtgctggtcagcgacacgttgtcctggctgggcaggtccagctcccggaggacctg
gggcttcagcttcccgtagcgctggctgcagtgacggatgctcttgcgctgccatttctg
ggtgctgtcactgtccttgctcactccaaaccagttcggcggtccccctgcggatggtct
gtgttgatggacgtttgggctttgcagcaccggccgccgagttcatggtngggtnaagag
atttgggttttttcn

Data files

   None.

Notes

   This description of what you can do when reading or writing files is
   not specific to the program seqret. All EMBOSS programs that read or
   write sequences can do the same.

   seqret is often one of the first programs taught in EMBOSS training
   courses. This is because it is versatile, it is extremely powerful for
   its size (17 lines of code) it illustrates many aspects of EMBOSS
   programs and it was one of the first EMBOSS programs to be written, so
   it has a special place in the hearts of EMBOSS developers.

   The name 'seqret' derives both from its function ("sequence return")
   and from the fact that immense amounts of functionality can come from
   so few lines of source code - most of the work is done by the EMBOSS
   libraries which the program calls and whose complexity is hidden, or
   "secret".

   The simplicity of the above description of this program greatly
   understates the rich functionality of this program.

   Because EMBOSS programs can take a wide range of qualifiers that
   slightly change the behaviour of the program when reading or writing a
   sequence, this program can do many more things than simply "read and
   write a sequence".

   seqret can read a sequence or many sequences from databases, files,
   files of sequence names, the command-line or the output of other
   programs and then can write them to files, the screen or pass them to
   other programs. Because it can read in a sequence from a database and
   write it to a file, seqret is a program for extracting sequences from
   databases. Because it can write the sequence to the screen, seqret is a
   program for displaying sequences.

   seqret can read sequences in any of a wide range of standard sequence
   formats. You can specify the input and output formats being used. If
   you don't specify the input format, seqret will try a set of possible
   formats until it reads it in successfully. Because you can specify the
   output sequence format, seqret is a program to reformat a sequence.

   seqret can read in the reverse complement of a nucleic acid sequence.
   It therefore is a program for producing the reverse complement of a
   sequence.

   seqret can read in a sequence whose begin and end positions you have
   specified and write out that fragment. It is therefore a utility for
   doing simple extraction of a region of a sequence.

   seqret can change the case of the sequence being read in to upper or to
   lower case. It is therefore a simple sequence beautification utility.

   seqret can do any combination of the above functions.

   The sequence input and output specification of this (and many other
   EMBOSS programs) is described as being a Uniform Sequence Address.

   The Uniform Sequence Address, or USA, is a somewhat tongue-in-cheek
   reference to a URL-style sequence naming used by all EMBOSS
   applications.

   The USA is a very flexible way of specifying one or more sequences from
   a variety of sources and includes sequence files, database queries and
   external applications.

   See the full specification of USA syntax at:
   http://emboss.sourceforge.net/docs/themes/UniformSequenceAddress.html

   The basic USA syntax is one of:
     * "file"
     * "file:entry"
     * "format::file"
     * "format::file:entry"
     * "database:entry"
     * "database"
     * "@file"

   Note that ':' separates the name of a file containing many possible
   entries from the specific name of a sequence entry in that file. It
   also separates the name of a database from an entry in that database

   Note also that '::' separates the specified format of a file from the
   name of the file. Normally the format can be omitted, in which case the
   program will attempt to identify the correct format when reading the
   sequence in and will default to using FASTA format when writing the
   sequence out.

   Valid names of the databases set up in your local implementation of
   EMBOSS can be seen by using the program 'showdb'.

   Database queries, and individual entries in files that have more than
   one sequence entry, use wildcards of "?" for any character and "*" for
   any string of characters. There are some problems with the Unix shell
   catching these characters so they do need to be hidden in quotes or
   preceded by a backslash on the Unix command line, (for example
   "embl:hs\*")

   The output USA name 'stdout' is special. It makes the output go to the
   device 'standard output'. This is the screen, by default.

  Example USAs

   The following are valid USAs for sequences:

   USA Description
   xxx.seq A sequence file "xxx.seq" in any format
   fasta::xxx.seq A sequence file "xxx.seq" in fasta format
   gcg::egmsmg.gcg A sequence file "egmsmg.gcg" in GCG 9 format
   egmsmg.gcg -sformat=gcg A sequence file "egmsmg.gcg" in GCG 9 format
   embl::x13776.em A sequence file "x13776.em" in EMBL format
   embl:x13776 EMBL entry X13776, using whatever access method is defined
   locally for the EMBL database
   embl:K01793 EMBL entry K01793, using whatever access method is defined
   locally for the EMBL database and searching by accession number and
   entry name (K01793 is a secondary accession number in this case for
   entry J01636)
   embl-acc:K01793 EMBL entry X13776, using whatever access method is
   defined locally for the EMBL database and searching by accession number
   only
   embl-id:x13776 EMBL entry x13776, using whatever access method is
   defined locally for the EMBL database, and searching by ID only
   embl:v0029* EMBL entries V00290, V00291, and so on, usually in
   alphabetical order, using whatever access method is defined locally for
   the EMBL database
   embl or EMBL:* All sequences in the EMBL database
   @mylist Reads file mylist and uses each line as a separate USA. This is
   standard VMS list file syntax, also used in SRS 4.0 but missing in SRS
   5.0 onwards. The list file is a list of USAs (one per line). List files
   can contain references to other lists files or any other standard USA.
   list::mylist Same as "@mylist" above
   'getz -e [embl-id:x13776] |' The pipe character "|" causes EMBOSS to
   fire up getz (SRS) to extract entry x13776 from EMBL in EMBL format.
   Any application or script which writes one or more sequences to stdout
   can be used in this way.
   asis::atacgcagttatctgaccat So far the shortest USA we could invent. In
   'asis' format the name is the sequence so no file needs to be opened.
   This is a special case. It was intended as a joke, but has proved quite
   useful for generating command lines when testing.

  Input sequence formats

   The input is a standard EMBOSS sequence query (also known as a 'USA').

   Major sequence database sources defined as standard in EMBOSS
   installations include srs:embl, srs:uniprot and ensembl

   Data can also be read from sequence output in any supported format
   written by an EMBOSS or third-party application.

   The input format can be specified by using the command-line qualifier
   -sformat xxx, where 'xxx' is replaced by the name of the required
   format. The available format names are: gff (gff3), gff2, embl (em),
   genbank (gb, refseq), ddbj, refseqp, pir (nbrf), swissprot (swiss, sw),
   dasgff and debug.

   See: http://emboss.sf.net/docs/themes/SequenceFormats.html for further
   information on sequence formats.

  Output sequence formats

   The output is a standard EMBOSS sequence file.

   The results can be output in one of several styles by using the
   command-line qualifier -osformat xxx, where 'xxx' is replaced by the
   name of the required format. The available format names are: embl,
   genbank, gff, pir, swiss, dasgff, debug, listfile, dbmotif, diffseq,
   excel, feattable, motif, nametable, regions, seqtable, simple, srs,
   table, tagseq.

   See: http://emboss.sf.net/docs/themes/SequenceFormats.html for further
   information on sequence formats.

  Future directions

   More formats, both for input and for output, can be easily added, so
   suggestions are always welcome.

  Associated qualifiers

   As noted previously there are many 'associated' qualifiers that alter
   the behaviour of seqret when it reads in or writes out a sequence. As
   these are used in all EMBOSS programs that read in or write out
   sequences, they are not reported by the '-help' qualifier. They are
   however reported by the pair of qualifiers: '-help -verbose':

   Some of the more useful associated qualifiers are:

   Qualifier                      Description
   -sbegin   The first position to be used in the sequence
   -send     The last position to be used in the sequence
   -sreverse Use the reverse complement of a nucleic acid sequence
   -sask     Ask the user for begin/end/reverse information
   -slower   Convert the sequence to lower case
   -supper   Convert the sequence to upper case
   -sformat  Specify the input sequence format
   -osformat Specify the output sequence format
   -ossingle Write each entry into a separate file

   The set of associated qualifiers for sequences behave in different ways
   depending on where they appear.

   If these qualifiers immediately follow a parameter they apply only to
   that parameter and not to all cases. If they occur before any
   parameters, they apply to all following sequence parameters.

   If there are no two parameters of equal type, the order of parameters
   and their qualifiers is irrelevant.

   Where a qualifier is defined more than once, for example "-sformat" for
   2 input sequences to be aligned, the qualifier name can have a number
   to indicate which sequence is meant. "-sbegin2=25" will apply only to
   the second sequence, no matter where it appears on the command line.

   The -sbegin and -send qualifiers take an integer number specifying the
   position to begin or end reading a sequence. If the number is positive,
   the number is the position counting from the first base or residue of
   the sequence. If the number is negative the position is counted from
   the end of the sequence, so position -1 is the last base or residue of
   the sequence. (If -sbegin 0 is used, it is assumed to be the same as
   -sbegin 1 and -send 0 is the same as -send -1.)

   The filter qualifier makes the program behave like a filter, reading
   its (first) input 'file' from the standard input, and writing its
   (first) output 'file' to the standard output. The -filter qualifier
   will also invoke the -auto qualifier, so the user is never prompted for
   any missing values.

   Example:

% cat sequence.seq | seqret -filter | lpr


   The example shows the application seqret being run with the -filter
   qualifier. The input file is 'piped' into the program using the unix
   command cat and the output is 'piped' directly to the unix program lpr,
   which will print it on the printer.

   When the -options qualifier is used and not all the parameters are
   given on the command line, it will query the user for those parameters.
   It will not only query the user for the required parameters as it would
   do without the -options qualifier, but it will also query the user for
   the optional parameters.

   When the -stdout qualifier is used, the user will still be prompted for
   all the info that is required, but will write to standard output by
   default. The user will also still be prompted for an output filename,
   in case the user wants to save the output to a file.

References

   None.

Warnings

   None.

Diagnostic Error Messages

   None.

Exit status

   It always exits with a status of 0.

Known bugs

   None.

See also

   Program name     Description
   aligncopy        Read and write alignments
   aligncopypair    Read and write pairs from alignments
   biosed           Replace or delete sequence sections
   codcopy          Copy and reformat a codon usage table
   cutseq           Remove a section from a sequence
   degapseq         Remove non-alphabetic (e.g. gap) characters from sequences
   descseq          Alter the name or description of a sequence
   entret           Retrieve sequence entries from flatfile databases and files
   extractalign     Extract regions from a sequence alignment
   extractfeat      Extract features from sequence(s)
   extractseq       Extract regions from a sequence
   featcopy         Read and write a feature table
   featmerge        Merge two overlapping feature tables
   featreport       Read and write a feature table
   feattext         Return a feature table original text
   listor           Write a list file of the logical OR of two sets of sequences
   makenucseq       Create random nucleotide sequences
   makeprotseq      Create random protein sequences
   maskambignuc     Mask all ambiguity characters in nucleotide sequences with
                    N
   maskambigprot    Mask all ambiguity characters in protein sequences with X
   maskfeat         Write a sequence with masked features
   maskseq          Write a sequence with masked regions
   newseq           Create a sequence file from a typed-in sequence
   nohtml           Remove mark-up (e.g. HTML tags) from an ASCII text file
   noreturn         Remove carriage return from ASCII files
   nospace          Remove whitespace from an ASCII text file
   notab            Replace tabs with spaces in an ASCII text file
   notseq           Write to file a subset of an input stream of sequences
   nthseq           Write to file a single sequence from an input stream of
                    sequences
   nthseqset        Read and write (return) one set of sequences from many
   pasteseq         Insert one sequence into another
   revseq           Reverse and complement a nucleotide sequence
   seqcount         Read and count sequences
   seqretsetall     Read and write (return) many sets of sequences
   seqretsplit      Read sequences and write them to individual files
   sizeseq          Sort sequences by size
   skipredundant    Remove redundant sequences from an input set
   skipseq          Read and write (return) sequences, skipping first few
   splitsource      Split sequence(s) into original source sequences
   splitter         Split sequence(s) into smaller sequences
   trimest          Remove poly-A tails from nucleotide sequences
   trimseq          Remove unwanted characters from start and end of sequence(s)
   trimspace        Remove extra whitespace from an ASCII text file
   union            Concatenate multiple sequences into a single sequence
   vectorstrip      Remove vectors from the ends of nucleotide sequence(s)
   yank             Add a sequence reference (a full USA) to a list file

   Valid names of the databases set up in your local implementation of
   EMBOSS can be seen by using the program 'showdb'.

Author(s)

   Peter Rice
   European Bioinformatics Institute, Wellcome Trust Genome Campus,
   Hinxton, Cambridge CB10 1SD, UK

   Please report all bugs to the EMBOSS bug team
   (emboss-bug (c) emboss.open-bio.org) not to the original author.

History

   1999 - Written by Peter Rice
   Feb 2002 - '-feature' qualifier added by Peter Rice

Target users

   This program is intended to be used by everyone and everything, from
   naive users to embedded scripts.

Comments

  Fasta output format

    Question

   When i tried to convert the EMBL format file into fasta format using
   the program "seqret", I found that the Access.no appears twice...

>AF102796 AF102796 Homo sapiens alphaE-catenin (CTNNA1) gene, exon 11.

    Answer

   "It is not a bug ... it is a feature"

   There are many "FASTA formats". EMBOSS uses the format that ACEDB and
   the EBI genome projects use. The first field after the ID is the
   accession number, so that accession numbers can be kept when sequences
   are converted to FASTA format, without using the NCBI format (with '|'
   characters in the IDs).

   Your EMBL format file has IDs that look like accession numbers, so
   EMBOSS fills in the accession number for each sequence, and reports it
   in the FASTA format.