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|
skipseq
Function
Reads and writes (returns) sequences, skipping first few
Description
skipseq skips the first few sequences in a multiple set of sequences,
and writes out the rest of them.
skipseq is a variant of the standard program for reading and writing
sequences, seqret.
seqret has an option to allow it to only read the first sequence from
a multiple set of sequences (-firstonly). seqret cannot, however, skip
the first few sequences from a multiple set of sequence, writing out
the rest; this is what skipseq is for.
In all other respects, skipseq is the same as seqret.
Usage
Here is a sample session with skipseq
This does not skip any sequences. It is exactly equivalent to seqret:
% skipseq
Reads and writes (returns) sequences, skipping first few
Input (gapped) sequence(s): @eclac.list
Number of sequences to skip at start [0]:
output sequence(s) [j01636.fasta]:
Go to the input files for this example
Go to the output files for this example
Example 2
This skips the first input sequence, writing out the others:
% skipseq -skip 1
Reads and writes (returns) sequences, skipping first few
Input (gapped) sequence(s): @eclac.list
output sequence(s) [j01636.fasta]:
Go to the output files for this example
Command line arguments
Standard (Mandatory) qualifiers:
[-sequence] seqall (Gapped) sequence(s) filename and optional
format, or reference (input USA)
-skip integer [0] Number of sequences to skip at start
(Any integer value)
[-outseq] seqoutall [.] Sequence set(s)
filename and optional format (output USA)
Additional (Optional) qualifiers: (none)
Advanced (Unprompted) qualifiers:
-feature boolean Use feature information
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
-sformat1 string Input sequence format
-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 standard output
-filter boolean Read standard input, write 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. 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
Input file format
skipseq reads one or more sequence USAs.
Input files for usage example
File: eclac.list
#Formerly ECLAC
tembl:J01636
#Formerly ECLACA
tembl:X51872
#Formerly ECLACI
tembl:V00294
#Formerly ECLACY
tembl:V00295
#Formerly ECLACZ
tembl:V00296
See the documentation for seqret to see the full range of things that
you can do when reading and writing sequences.
Output file format
skipseq writes one or more sequences files, having optionally skipped
the first few sequences.
Output files for usage example
File: j01636.fasta
>J01636 J01636.1 E.coli lactose operon with lacI, lacZ, lacY and lacA genes.
gacaccatcgaatggcgcaaaacctttcgcggtatggcatgatagcgcccggaagagagt
caattcagggtggtgaatgtgaaaccagtaacgttatacgatgtcgcagagtatgccggt
gtctcttatcagaccgtttcccgcgtggtgaaccaggccagccacgtttctgcgaaaacg
cgggaaaaagtggaagcggcgatggcggagctgaattacattcccaaccgcgtggcacaa
caactggcgggcaaacagtcgttgctgattggcgttgccacctccagtctggccctgcac
gcgccgtcgcaaattgtcgcggcgattaaatctcgcgccgatcaactgggtgccagcgtg
gtggtgtcgatggtagaacgaagcggcgtcgaagcctgtaaagcggcggtgcacaatctt
ctcgcgcaacgcgtcagtgggctgatcattaactatccgctggatgaccaggatgccatt
gctgtggaagctgcctgcactaatgttccggcgttatttcttgatgtctctgaccagaca
cccatcaacagtattattttctcccatgaagacggtacgcgactgggcgtggagcatctg
gtcgcattgggtcaccagcaaatcgcgctgttagcgggcccattaagttctgtctcggcg
cgtctgcgtctggctggctggcataaatatctcactcgcaatcaaattcagccgatagcg
gaacgggaaggcgactggagtgccatgtccggttttcaacaaaccatgcaaatgctgaat
gagggcatcgttcccactgcgatgctggttgccaacgatcagatggcgctgggcgcaatg
cgcgccattaccgagtccgggctgcgcgttggtgcggatatctcggtagtgggatacgac
gataccgaagacagctcatgttatatcccgccgtcaaccaccatcaaacaggattttcgc
ctgctggggcaaaccagcgtggaccgcttgctgcaactctctcagggccaggcggtgaag
ggcaatcagctgttgcccgtctcactggtgaaaagaaaaaccaccctggcgcccaatacg
caaaccgcctctccccgcgcgttggccgattcattaatgcagctggcacgacaggtttcc
cgactggaaagcgggcagtgagcgcaacgcaattaatgtgagttagctcactcattaggc
accccaggctttacactttatgcttccggctcgtatgttgtgtggaattgtgagcggata
acaatttcacacaggaaacagctatgaccatgattacggattcactggccgtcgttttac
aacgtcgtgactgggaaaaccctggcgttacccaacttaatcgccttgcagcacatcccc
ctttcgccagctggcgtaatagcgaagaggcccgcaccgatcgcccttcccaacagttgc
gcagcctgaatggcgaatggcgctttgcctggtttccggcaccagaagcggtgccggaaa
gctggctggagtgcgatcttcctgaggccgatactgtcgtcgtcccctcaaactggcaga
tgcacggttacgatgcgcccatctacaccaacgtaacctatcccattacggtcaatccgc
cgtttgttcccacggagaatccgacgggttgttactcgctcacatttaatgttgatgaaa
gctggctacaggaaggccagacgcgaattatttttgatggcgttaactcggcgtttcatc
tgtggtgcaacgggcgctgggtcggttacggccaggacagtcgtttgccgtctgaatttg
acctgagcgcatttttacgcgccggagaaaaccgcctcgcggtgatggtgctgcgttgga
gtgacggcagttatctggaagatcaggatatgtggcggatgagcggcattttccgtgacg
tctcgttgctgcataaaccgactacacaaatcagcgatttccatgttgccactcgcttta
atgatgatttcagccgcgctgtactggaggctgaagttcagatgtgcggcgagttgcgtg
actacctacgggtaacagtttctttatggcagggtgaaacgcaggtcgccagcggcaccg
cgcctttcggcggtgaaattatcgatgagcgtggtggttatgccgatcgcgtcacactac
gtctgaacgtcgaaaacccgaaactgtggagcgccgaaatcccgaatctctatcgtgcgg
tggttgaactgcacaccgccgacggcacgctgattgaagcagaagcctgcgatgtcggtt
tccgcgaggtgcggattgaaaatggtctgctgctgctgaacggcaagccgttgctgattc
gaggcgttaaccgtcacgagcatcatcctctgcatggtcaggtcatggatgagcagacga
tggtgcaggatatcctgctgatgaagcagaacaactttaacgccgtgcgctgttcgcatt
atccgaaccatccgctgtggtacacgctgtgcgaccgctacggcctgtatgtggtggatg
aagccaatattgaaacccacggcatggtgccaatgaatcgtctgaccgatgatccgcgct
ggctaccggcgatgagcgaacgcgtaacgcgaatggtgcagcgcgatcgtaatcacccga
gtgtgatcatctggtcgctggggaatgaatcaggccacggcgctaatcacgacgcgctgt
atcgctggatcaaatctgtcgatccttcccgcccggtgcagtatgaaggcggcggagccg
acaccacggccaccgatattatttgcccgatgtacgcgcgcgtggatgaagaccagccct
tcccggctgtgccgaaatggtccatcaaaaaatggctttcgctacctggagagacgcgcc
cgctgatcctttgcgaatacgcccacgcgatgggtaacagtcttggcggtttcgctaaat
[Part of this file has been deleted for brevity]
gttacccaacttaatcgccttgcagcacatccccctttcgccagctggcgtaatagcgaa
gaggcccgcaccgatcgcccttcccaacagttgcgcagcctgaatggcgaatggcgcttt
gcctggtttccggcaccagaagcggtgccggaaagctggctggagtgcgatcttcctgag
gccgatactgtcgtcgtcccctcaaactggcagatgcacggttacgatgcgcccatctac
accaacgtaacctatcccattacggtcaatccgccgtttgttcccacggagaatccgacg
ggttgttactcgctcacatttaatgttgatgaaagctggctacaggaaggccagacgcga
attatttttgatggcgttaactcggcgtttcatctgtggtgcaacgggcgctgggtcggt
tacggccaggacagtcgtttgccgtctgaatttgacctgagcgcatttttacgcgccgga
gaaaaccgcctcgcggtgatggtgctgcgttggagtgacggcagttatctggaagatcag
gatatgtggcggatgagcggcattttccgtgacgtctcgttgctgcataaaccgactaca
caaatcagcgatttccatgttgccactcgctttaatgatgatttcagccgcgctgtactg
gaggctgaagttcagatgtgcggcgagttgcgtgactacctacgggtaacagtttcttta
tggcagggtgaaacgcaggtcgccagcggcaccgcgcctttcggcggtgaaattatcgat
gagcgtggtggttatgccgatcgcgtcacactacgtctgaacgtcgaaaacccgaaactg
tggagcgccgaaatcccgaatctctatcgtgcggtggttgaactgcacaccgccgacggc
acgctgattgaagcagaagcctgcgatgtcggtttccgcgaggtgcggattgaaaatggt
ctgctgctgctgaacggcaagccgttgctgattcgaggcgttaaccgtcacgagcatcat
cctctgcatggtcaggtcatggatgagcagacgatggtgcaggatatcctgctgatgaag
cagaacaactttaacgccgtgcgctgttcgcattatccgaaccatccgctgtggtacacg
ctgtgcgaccgctacggcctgtatgtggtggatgaagccaatattgaaacccacggcatg
gtgccaatgaatcgtctgaccgatgatccgcgctggctaccggcgatgagcgaacgcgta
acgcgaatggtgcagcgcgatcgtaatcacccgagtgtgatcatctggtcgctggggaat
gaatcaggccacggcgctaatcacgacgcgctgtatcgctggatcaaatctgtcgatcct
tcccgcccggtgcagtatgaaggcggcggagccgacaccacggccaccgatattatttgc
ccgatgtacgcgcgcgtggatgaagaccagcccttcccggctgtgccgaaatggtccatc
aaaaaatggctttcgctacctggagagacgcgcccgctgatcctttgcgaatacgcccac
gcgatgggtaacagtcttggcggtttcgctaaatactggcaggcgtttcgtcagtatccc
cgtttacagggcggcttcgtctgggactgggtggatcagtcgctgattaaatatgatgaa
aacggcaacccgtggtcggcttacggcggtgattttggcgatacgccgaacgatcgccag
ttctgtatgaacggtctggtctttgccgaccgcacgccgcatccagcgctgacggaagca
aaacaccagcagcagtttttccagttccgtttatccgggcaaaccatcgaagtgaccagc
gaatacctgttccgtcatagcgataacgagctcctgcactggatggtggcgctggatggt
aagccgctggcaagcggtgaagtgcctctggatgtcgctccacaaggtaaacagttgatt
gaactgcctgaactaccgcagccggagagcgccgggcaactctggctcacagtacgcgta
gtgcaaccgaacgcgaccgcatggtcagaagccgggcacatcagcgcctggcagcagtgg
cgtctggcggaaaacctcagtgtgacgctccccgccgcgtcccacgccatcccgcatctg
accaccagcgaaatggatttttgcatcgagctgggtaataagcgttggcaatttaaccgc
cagtcaggctttctttcacagatgtggattggcgataaaaaacaactgctgacgccgctg
cgcgatcagttcacccgtgcaccgctggataacgacattggcgtaagtgaagcgacccgc
attgaccctaacgcctgggtcgaacgctggaaggcggcgggccattaccaggccgaagca
gcgttgttgcagtgcacggcagatacacttgctgatgcggtgctgattacgaccgctcac
gcgtggcagcatcaggggaaaaccttatttatcagccggaaaacctaccggattgatggt
agtggtcaaatggcgattaccgttgatgttgaagtggcgagcgatacaccgcatccggcg
cggattggcctgaactgccagctggcgcaggtagcagagcgggtaaactggctcggatta
gggccgcaagaaaactatcccgaccgccttactgccgcctgttttgaccgctgggatctg
ccattgtcagacatgtataccccgtacgtcttcccgagcgaaaacggtctgcgctgcggg
acgcgcgaattgaattatggcccacaccagtggcgcggcgacttccagttcaacatcagc
cgctacagtcaacagcaactgatggaaaccagccatcgccatctgctgcacgcggaagaa
ggcacatggctgaatatcgacggtttccatatggggattggtggcgacgactcctggagc
ccgtcagtatcggcggaattccagctgagcgccggtcgctaccattaccagttggtctgg
tgtcaaaaataataataa
Output files for usage example 2
File: j01636.fasta
>X51872 X51872.1 Escherichia coli lacA gene for thiogalactoside transacetylase
gtgaatgaagtcgcttaagcaatcaatgtcggatgcggcgcgacgcttatccgaccaaca
tatcataacggagtgatcgcattgaacatgccaatgaccgaaagaataagagcaggcaag
ctatttaccgatatgtgcgaaggcttaccggaaaaaagacttcgtgggaaaacgttaatg
tatgagtttaatcactcgcatccatcagaagttgaaaaaagagaaagcctgattaaagaa
atgtttgccacggtaggggaaaacgcctgggtagaaccgcctgtctatttctcttacggt
tccaacatccatataggccgcaatttttatgcaaatttcaatttaaccattgtcgatgac
tacacggtaacaatcggtgataacgtactgattgcacccaacgttactctttccgttacg
ggacaccctgtacaccatgaattgagaaaaaacggcgagatgtactcttttccgataacg
attggcaataacgtctggatcggaagtcatgtggttattaatccaggcgtcaccatcggg
gataattctgttattggcgcgggtagtatcgtcacaaaagacattccaccaaacgtcgtg
gcggctggcgttccttgtcgggttattcgcgaaataaacgaccgggataagcactattat
ttcaaagattataaagttgaatcgtcagtttaaattataaaaattgcctgatacgctgcg
cttatcaggcctacaagttcagcgatctacattagccgcatccggcatgaacaaagcgca
ggaacaagcgtcgcatcatgcctctttgacccacagctgcggaaaacgtactggtgcaaa
acgcagggttatgatcatcagcccaacgacgcacagcgcatgaaatgcccagtccatcag
gtaattgccgctgatactacgcagcacgccagaaaaccacggggcaagcccggcgatgat
aaaaccgattccctgcataaacgccaccagcttgccagcaatagccggttgcacagagtg
atcgagcgccagcagcaaacagagcggaaacgcgccgcccagacctaacccacacaccat
cgcccacaataccggcaattgcatcggcagccagataaagccgcagaaccccaccagttg
taacaccagcgccagcattaacagtttgcgccgatcctgatggcgagccatagcaggcat
cagcaaagctcctgcggcttgcccaagcgtcatcaatgccagtaaggaaccgctgtactg
cgcgctggcaccaatctcaatatagaaagcgggtaaccaggcaatcaggctggcgtaacc
gccgttaatcagaccgaagtaaacacccagcgtccacgcgcggggagtgaataccacgcg
aaccggagtggttgttgtcttgtgggaagaggcgacctcgcgggcgctttgccaccacca
ggcaaagagcgcaacaacggcaggcagcgccaccaggcgagtgtttgataccaggtttcg
ctatgttgaactaaccagggcgttatggcggcaccaagcccaccgccgcccatcagagcc
gcggaccacagccccatcaccagtggcgtgcgctgctgaaaccgccgtttaatcaccgaa
gcatcaccgcctgaatgatgccgatccccaccccaccaagcagtgcgctgctaagcagca
gcgcactttgcgggtaaagctcacgcatcaatgcaccgacggcaatcagcaacagactga
tggcgacactgcgacgttcgctgacatgctgatgaagccagcttccggccagcgccagcc
cgcccatggtaaccaccggcagagcggtcgac
>V00294 V00294.1 E. coli laci gene (codes for the lac repressor).
ccggaagagagtcaattcagggtggtgaatgtgaaaccagtaacgttatacgatgtcgca
gagtatgccggtgtctcttatcagaccgtttcccgcgtggtgaaccaggccagccacgtt
tctgcgaaaacgcgggaaaaagtggaagcggcgatggcggagctgaattacattcccaac
cgcgtggcacaacaactggcgggcaaacagtcgttgctgattggcgttgccacctccagt
ctggccctgcacgcgccgtcgcaaattgtcgcggcgattaaatctcgcgccgatcaactg
ggtgccagcgtggtggtgtcgatggtagaacgaagcggcgtcgaagcctgtaaagcggcg
gtgcacaatcttctcgcgcaacgcgtcagtgggctgatcattaactatccgctggatgac
caggatgccattgctgtggaagctgcctgcactaatgttccggcgttatttcttgatgtc
tctgaccagacacccatcaacagtattattttctcccatgaagacggtacgcgactgggc
gtggagcatctggtcgcattgggtcaccagcaaatcgcgctgttagcgggcccattaagt
tctgtctcggcgcgtctgcgtctggctggctggcataaatatctcactcgcaatcaaatt
cagccgatagcggaacgggaaggcgactggagtgccatgtccggttttcaacaaaccatg
caaatgctgaatgagggcatcgttcccactgcgatgctggttgccaacgatcagatggcg
ctgggcgcaatgcgcgccattaccgagtccgggctgcgcgttggtgcggatatctcggta
gtgggatacgacgataccgaagacagctcatgttatatcccgccgtcaaccaccatcaaa
caggattttcgcctgctggggcaaaccagcgtggaccgcttgctgcaactctctcagggc
caggcggtgaagggcaatcagctgttgcccgtctcactggtgaaaagaaaaaccaccctg
[Part of this file has been deleted for brevity]
gttacccaacttaatcgccttgcagcacatccccctttcgccagctggcgtaatagcgaa
gaggcccgcaccgatcgcccttcccaacagttgcgcagcctgaatggcgaatggcgcttt
gcctggtttccggcaccagaagcggtgccggaaagctggctggagtgcgatcttcctgag
gccgatactgtcgtcgtcccctcaaactggcagatgcacggttacgatgcgcccatctac
accaacgtaacctatcccattacggtcaatccgccgtttgttcccacggagaatccgacg
ggttgttactcgctcacatttaatgttgatgaaagctggctacaggaaggccagacgcga
attatttttgatggcgttaactcggcgtttcatctgtggtgcaacgggcgctgggtcggt
tacggccaggacagtcgtttgccgtctgaatttgacctgagcgcatttttacgcgccgga
gaaaaccgcctcgcggtgatggtgctgcgttggagtgacggcagttatctggaagatcag
gatatgtggcggatgagcggcattttccgtgacgtctcgttgctgcataaaccgactaca
caaatcagcgatttccatgttgccactcgctttaatgatgatttcagccgcgctgtactg
gaggctgaagttcagatgtgcggcgagttgcgtgactacctacgggtaacagtttcttta
tggcagggtgaaacgcaggtcgccagcggcaccgcgcctttcggcggtgaaattatcgat
gagcgtggtggttatgccgatcgcgtcacactacgtctgaacgtcgaaaacccgaaactg
tggagcgccgaaatcccgaatctctatcgtgcggtggttgaactgcacaccgccgacggc
acgctgattgaagcagaagcctgcgatgtcggtttccgcgaggtgcggattgaaaatggt
ctgctgctgctgaacggcaagccgttgctgattcgaggcgttaaccgtcacgagcatcat
cctctgcatggtcaggtcatggatgagcagacgatggtgcaggatatcctgctgatgaag
cagaacaactttaacgccgtgcgctgttcgcattatccgaaccatccgctgtggtacacg
ctgtgcgaccgctacggcctgtatgtggtggatgaagccaatattgaaacccacggcatg
gtgccaatgaatcgtctgaccgatgatccgcgctggctaccggcgatgagcgaacgcgta
acgcgaatggtgcagcgcgatcgtaatcacccgagtgtgatcatctggtcgctggggaat
gaatcaggccacggcgctaatcacgacgcgctgtatcgctggatcaaatctgtcgatcct
tcccgcccggtgcagtatgaaggcggcggagccgacaccacggccaccgatattatttgc
ccgatgtacgcgcgcgtggatgaagaccagcccttcccggctgtgccgaaatggtccatc
aaaaaatggctttcgctacctggagagacgcgcccgctgatcctttgcgaatacgcccac
gcgatgggtaacagtcttggcggtttcgctaaatactggcaggcgtttcgtcagtatccc
cgtttacagggcggcttcgtctgggactgggtggatcagtcgctgattaaatatgatgaa
aacggcaacccgtggtcggcttacggcggtgattttggcgatacgccgaacgatcgccag
ttctgtatgaacggtctggtctttgccgaccgcacgccgcatccagcgctgacggaagca
aaacaccagcagcagtttttccagttccgtttatccgggcaaaccatcgaagtgaccagc
gaatacctgttccgtcatagcgataacgagctcctgcactggatggtggcgctggatggt
aagccgctggcaagcggtgaagtgcctctggatgtcgctccacaaggtaaacagttgatt
gaactgcctgaactaccgcagccggagagcgccgggcaactctggctcacagtacgcgta
gtgcaaccgaacgcgaccgcatggtcagaagccgggcacatcagcgcctggcagcagtgg
cgtctggcggaaaacctcagtgtgacgctccccgccgcgtcccacgccatcccgcatctg
accaccagcgaaatggatttttgcatcgagctgggtaataagcgttggcaatttaaccgc
cagtcaggctttctttcacagatgtggattggcgataaaaaacaactgctgacgccgctg
cgcgatcagttcacccgtgcaccgctggataacgacattggcgtaagtgaagcgacccgc
attgaccctaacgcctgggtcgaacgctggaaggcggcgggccattaccaggccgaagca
gcgttgttgcagtgcacggcagatacacttgctgatgcggtgctgattacgaccgctcac
gcgtggcagcatcaggggaaaaccttatttatcagccggaaaacctaccggattgatggt
agtggtcaaatggcgattaccgttgatgttgaagtggcgagcgatacaccgcatccggcg
cggattggcctgaactgccagctggcgcaggtagcagagcgggtaaactggctcggatta
gggccgcaagaaaactatcccgaccgccttactgccgcctgttttgaccgctgggatctg
ccattgtcagacatgtataccccgtacgtcttcccgagcgaaaacggtctgcgctgcggg
acgcgcgaattgaattatggcccacaccagtggcgcggcgacttccagttcaacatcagc
cgctacagtcaacagcaactgatggaaaccagccatcgccatctgctgcacgcggaagaa
ggcacatggctgaatatcgacggtttccatatggggattggtggcgacgactcctggagc
ccgtcagtatcggcggaattccagctgagcgccggtcgctaccattaccagttggtctgg
tgtcaaaaataataataa
See the documentation for seqret to see the full range of things that
you can do when reading and writing sequences.
Data files
None.
Notes
None.
References
None.
Warnings
You may skip all of the input files.
If the -skip value is greater than or equal to the number of input
sequences, there is no warning: this is legal.
Diagnostic Error Messages
None.
Exit status
It always exits with status 0.
Known bugs
None.
See also
Program name Description
biosed Replace or delete sequence sections
codcopy Reads and writes a codon usage table
cutseq Removes a specified section from a sequence
degapseq Removes gap characters from sequences
descseq Alter the name or description of a sequence
entret Reads and writes (returns) flatfile entries
extractalign Extract regions from a sequence alignment
extractfeat Extract features from a sequence
extractseq Extract regions from a sequence
listor Write a list file of the logical OR of two sets of sequences
makenucseq Creates random nucleotide sequences
makeprotseq Creates random protein sequences
maskfeat Mask off features of a sequence
maskseq Mask off regions of a sequence
newseq Type in a short new sequence
noreturn Removes carriage return from ASCII files
notseq Exclude a set of sequences and write out the remaining ones
nthseq Writes one sequence from a multiple set of sequences
pasteseq Insert one sequence into another
revseq Reverse and complement a sequence
seqret Reads and writes (returns) sequences
seqretsplit Reads and writes (returns) sequences in individual files
splitter Split a sequence into (overlapping) smaller sequences
trimest Trim poly-A tails off EST sequences
trimseq Trim ambiguous bits off the ends of sequences
union Reads sequence fragments and builds one sequence
vectorstrip Strips out DNA between a pair of vector sequences
yank Reads a sequence range, appends the full USA to a list file
skipseq is a variant of the standard program for reading and writing
sequences, seqret.
Author(s)
Peter Rice (pmr ebi.ac.uk)
Informatics Division, European Bioinformatics Institute, Wellcome
Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
History
Written (25 June 2002) - Peter Rice
Target users
This program is intended to be used by everyone and everything, from
naive users to embedded scripts.
Comments
None
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