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<TITLE> EMBASSY: SEQSORT documentation. </TITLE>
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<H2> SEQSORT documentation
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<br><H2>CONTENTS </H2>
<b> <a href="#1.0">1.0 SUMMARY </a></b><br>
<b> <a href="#2.0">2.0 INPUTS & OUTPUTS </a></b><br>
<b> <a href="#3.0">3.0 INPUT FILE FORMAT </a></b><br>
<b> <a href="#4.0">4.0 OUTPUT FILE FORMAT </a></b><br>
<b> <a href="#5.0">5.0 DATA FILES </a></b><br>
<b> <a href="#6.0">6.0 USAGE </a></b><br>
<b> <a href="#7.0">7.0 KNOWN BUGS & WARNINGS </a></b><br>
<b> <a href="#8.0">8.0 NOTES </a></b><br>
<b> <a href="#9.0">9.0 DESCRIPTION </a></b><br>
<b> <a href="#10.0">10.0 ALGORITHM </a></b><br>
<b> <a href="#11.0">11.0 RELATED APPLICATIONS </a></b><br>
<b> <a href="#12.0">12.0 DIAGNOSTIC ERROR MESSAGES </a></b><br>
<b> <a href="#13.0">13.0 AUTHORS </a></b><br>
<b> <a href="#14.0">14.0 REFERENCES </a></b><br>
<!-- SUMMARY
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<a name="1.0"></a>
<br><br><br><H2> 1.0 SUMMARY </H2>
Remove ambiguous classified sequences from DHF files
<!-- INPUTS & OUTPUTS
Short summary of the application inputs and outputs in its different
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<a name="2.0"></a>
<br><br><br><H2> 2.0 INPUTS & OUTPUTS </H2>
SEQSORT reads a directory of DHF files (domain hits files) where each file contains hits to a single SCOP family, compares, processes and collates the hits and writes a directory of DHF files which contain only those hits that could be uniquely assigned to a SCOP family. Optionally, two further files of hits are written: (i) a domain families file, of ALL hits from the input files that could be uniquely assigned to a SCOP family and (ii) a domain ambiguities file, of hits from ALL the input files that are of ambiguous family assignment and are assigned as relatives to a SCOP superfamily or fold instead.
<br> The path for the domain hits files (input and output) and the names of the output files are specified by the user. The file extension of the DHF files are set in the ACD file.
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Use "<b>SEQSORT</b> reads any normal sequence USAs." if
appropriate.
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<a name="3.0"></a>
<br><br><br><H2> 3.0 INPUT FILE FORMAT </H2>
The format of the domain hits file is described in <a href="seqsearch.html">SEQSEARCH documentation.</a>
<!-- OUTPUT FILE FORMAT
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<a name="4.0"></a>
<br><br><br><H2> 4.0 OUTPUT FILE FORMAT </H2>
The format of the domain hits file is described in <a href="seqsearch.html">SEQSEARCH documentation.</a>
<br><br> The domain families file and domain ambiguities file also use the DHF format. Whereas normally a DHF file contains hits for a single node from SCOP or CATH, the families and ambiguities files may contain domains from multiple different families (domain families file), or superfamilies or folds (ambiguities file). Domains of the same node (e.g. family) will be grouped together in blocks, i.e. all hits for domain A, then all hits for domain B and so on (see Figure 1).
<a name="output.1"></a>
<h3>Output files for usage example </h3>
<p><h3>File: fam.dhf</h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
> Q9YBD5^.^1^95^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^.^56.10^0.000e+00^9.000e+00
VRKIRSGVVIDHIPPGRAFTMLKALGLLPPRGYRWRIAVVINAESSKLGRKDILKIEGYKPRQRDLEVLGIIAPGATFNVIEDYKVVEKVKLKLP
> Q97FS4^.^1^90^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^.^43.40^0.000e+00^6.000e+00
INSIKNGIVIDHIKAGHGIKIYNYLKLGEAEFPTALIMNAISKKNKAKDIIKIENVMDLDLAVLGFLDPNITVNIIEDEKIRQKIQLKLP
> Q7MX57^.^1^92^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^.^73.80^0.000e+00^5.000e+00
VAAIRNGIVIDHIPPTKLFKVATLLQLDDLDKRITIGNNLRSRSHGSKGVIKIEDKTFEEEELNRIALIAPNVRLNIIRDYEVVEKRQVEVP
> P96111^.^1^98^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^.^43.00^0.000e+00^9.000e+00
GIKPIENGTVIDHIAKGKTPEEIYSTILKIRKILRLYDVDSADGIFRSSDGSFKGYISLPDRYLSKKEIKKLSAISPNTTVNIIKNSTVVEKYRIKLP
> Q08462^.^1^167^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase catalytic domain^.^46.20^0.000e+00^4.000e+00
DCVCVMFASIPDFKEFYTESDVNKEGLECLRLLNEIIADFDDLLSKPKFSGVEKIKTIGSTYMAATGLSAVPSQEHSQEPERQYMHIGTMVEFAFALVGKLDAINKHSFNDFKLRVGINHGPVIAGVIGAQKPQYDIWGNTVNVASRMDSTGVLDKIQVTEETSLVL
> Q03101^.^1^149^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase catalytic domain^.^65.80^0.000e+00^4.000e+00
NNACVFFLDIAGFTRFSSIHSPEQVIQVLIKIFNSMDLLCAKHGIEKIKTIGDAYMATCGIFPKCDDIRHNTYKMLGFAMDVLEFIPKEMSFHLGLQVRVGIHCGPVISGVISGYAKPHFDVWGDTVNVASRMESTGIAGQIHVSDRVY
> Q02153^.^1^165^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase catalytic domain^.^68.90^0.000e+00^4.000e+00
HKRPVPAKRYDNVTILFSGIVGFNAFCSKHASGEGAMKIVNLLNDLYTRFDTLTDSRKNPFVYKVETVGDKYMTVSGLPEPCIHHARSICHLALDMMEIAGQVQVDGESVQITIGIHTGEVVTGVIGQRMPRYCLFGNTVNLTSRTETTGEKGKINVSEYTYRCL
> P46197^.^1^168^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase catalytic domain^.^78.50^0.000e+00^7.000e+00
VQAEAFDSVTIYFSDIVGFTALSAESTPMQVVTLLNDLYTCFDAIIDNFDVYKVETIGDAYMVVSGLPGRNGQRHAPEIARMALALLDAVSSFRIRHRPHDQLRLRIGVHTGPVCAGVVGLKMPRYCLFGDTVNTASRMESNGQALKIHVSSTTKDALDELGCFQLEL
> P40137^.^1^139^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase catalytic domain^.^48.50^0.000e+00^6.000e+00
VTLLFADIRDFTSLSERLRPEQVVTLLNEYYGRMVEVVFRHGGTLDKFIGDALMVYFGAPIADPAHARRGVQCALDMVQELETVNALRSARGEPCLRIGVGVHTGPAVLGNIGSATRRLEYTAIGDTVNLASRIESLTK
> P23466^.^1^154^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase catalytic domain^.^50.80^0.000e+00^1.000e+00
PTGNVAIVFTDIKNSTFLWELFPDAMRAAIKTHNDIMRRQLRIYGGYEVKTEGDAFMVAFPTPTSALVWCLSVQLKLLEAEWPEEITSIQDGCLITDNSGTKVYLGLSVRMGVHWGCPVPEIDLVTQRMDYLGPVVNKAARVSGVADGGQITLS
> O30820^.^1^149^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase catalytic domain^.^75.40^0.000e+00^6.000e+00
DEASVLFADIVGFTERASSTAPADLVRFLDRLYSAFDELVDQHGLEKIKVSGDSYMVVSGVPRPRPDHTQALADFALDMTNVAAQLKDPRGNPVPLRVGLATGPVVAGVVGSRRFFYDVWGDAVNVASRMESTDSVGQIQVPDEVYERL
</pre>
</td></tr></table><p>
<p><h3>File: oth.dhf</h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
</pre>
</td></tr></table><p>
<p><h3>File: 54894.dhf</h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
> Q9YBD5^.^1^95^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^.^56.10^0.000e+00^9.000e+00
VRKIRSGVVIDHIPPGRAFTMLKALGLLPPRGYRWRIAVVINAESSKLGRKDILKIEGYKPRQRDLEVLGIIAPGATFNVIEDYKVVEKVKLKLP
> Q97FS4^.^1^90^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^.^43.40^0.000e+00^6.000e+00
INSIKNGIVIDHIKAGHGIKIYNYLKLGEAEFPTALIMNAISKKNKAKDIIKIENVMDLDLAVLGFLDPNITVNIIEDEKIRQKIQLKLP
> Q7MX57^.^1^92^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^.^73.80^0.000e+00^5.000e+00
VAAIRNGIVIDHIPPTKLFKVATLLQLDDLDKRITIGNNLRSRSHGSKGVIKIEDKTFEEEELNRIALIAPNVRLNIIRDYEVVEKRQVEVP
> P96111^.^1^98^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^.^43.00^0.000e+00^9.000e+00
GIKPIENGTVIDHIAKGKTPEEIYSTILKIRKILRLYDVDSADGIFRSSDGSFKGYISLPDRYLSKKEIKKLSAISPNTTVNIIKNSTVVEKYRIKLP
</pre>
</td></tr></table><p>
<p><h3>File: 55074.dhf</h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
> Q08462^.^1^167^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase catalytic domain^.^46.20^0.000e+00^4.000e+00
DCVCVMFASIPDFKEFYTESDVNKEGLECLRLLNEIIADFDDLLSKPKFSGVEKIKTIGSTYMAATGLSAVPSQEHSQEPERQYMHIGTMVEFAFALVGKLDAINKHSFNDFKLRVGINHGPVIAGVIGAQKPQYDIWGNTVNVASRMDSTGVLDKIQVTEETSLVL
> Q03101^.^1^149^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase catalytic domain^.^65.80^0.000e+00^4.000e+00
NNACVFFLDIAGFTRFSSIHSPEQVIQVLIKIFNSMDLLCAKHGIEKIKTIGDAYMATCGIFPKCDDIRHNTYKMLGFAMDVLEFIPKEMSFHLGLQVRVGIHCGPVISGVISGYAKPHFDVWGDTVNVASRMESTGIAGQIHVSDRVY
> Q02153^.^1^165^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase catalytic domain^.^68.90^0.000e+00^4.000e+00
HKRPVPAKRYDNVTILFSGIVGFNAFCSKHASGEGAMKIVNLLNDLYTRFDTLTDSRKNPFVYKVETVGDKYMTVSGLPEPCIHHARSICHLALDMMEIAGQVQVDGESVQITIGIHTGEVVTGVIGQRMPRYCLFGNTVNLTSRTETTGEKGKINVSEYTYRCL
> P46197^.^1^168^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase catalytic domain^.^78.50^0.000e+00^7.000e+00
VQAEAFDSVTIYFSDIVGFTALSAESTPMQVVTLLNDLYTCFDAIIDNFDVYKVETIGDAYMVVSGLPGRNGQRHAPEIARMALALLDAVSSFRIRHRPHDQLRLRIGVHTGPVCAGVVGLKMPRYCLFGDTVNTASRMESNGQALKIHVSSTTKDALDELGCFQLEL
> P40137^.^1^139^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase catalytic domain^.^48.50^0.000e+00^6.000e+00
VTLLFADIRDFTSLSERLRPEQVVTLLNEYYGRMVEVVFRHGGTLDKFIGDALMVYFGAPIADPAHARRGVQCALDMVQELETVNALRSARGEPCLRIGVGVHTGPAVLGNIGSATRRLEYTAIGDTVNLASRIESLTK
> P23466^.^1^154^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase catalytic domain^.^50.80^0.000e+00^1.000e+00
PTGNVAIVFTDIKNSTFLWELFPDAMRAAIKTHNDIMRRQLRIYGGYEVKTEGDAFMVAFPTPTSALVWCLSVQLKLLEAEWPEEITSIQDGCLITDNSGTKVYLGLSVRMGVHWGCPVPEIDLVTQRMDYLGPVVNKAARVSGVADGGQITLS
> O30820^.^1^149^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase catalytic domain^.^75.40^0.000e+00^6.000e+00
DEASVLFADIVGFTERASSTAPADLVRFLDRLYSAFDELVDQHGLEKIKVSGDSYMVVSGVPRPRPDHTQALADFALDMTNVAAQLKDPRGNPVPLRVGLATGPVVAGVVGSRRFFYDVWGDAVNVASRMESTDSVGQIQVPDEVYERL
</pre>
</td></tr></table><p>
<!--
<br><br><b>Figure 1 Excerpt from a domain families file (output)</b>
<table><td bgcolor="#CFCCFF">
<pre>
> P00478^.^8^99^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^PSIBLAST^191.00^0.000e+00^0.000e+00
VEAIKRGTVIDHIPAQIGFKLLSLFKLTETDQRITIGLNLPSGEMGRKDLIKIENTFLSEDQVDQLALYAPQATVNRIDNYEVVGKSRPSLP
> O58452^.^6^99^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^PSIBLAST^94.30^0.000e+00^6.000e-20
VSAIKEGTVIDHIPAGKGLKVIEILGLSKLSNGGSVLLAMNVPSKKLGRKDIVKVEGKFLSEEEVNKIALVAPTATVNIIRNYKVVEKFKVEVP
> O30129^.^6^98^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^PSIBLAST^79.60^0.000e+00^2.000e-15
VSKIKEGTVIDHINAGKALLVLKILKIQPGTDLTVSMAMNVPSSKMGKKDIVKVEGMFIRDEELNKIALISPNATINLIRDYEIERKFKVSPP
> O26938^.^11^101^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^PSIBLAST^81.90^0.000e+00^3.000e-16
VKPIKNGTVIDHITANRSLNVLNILGLPDGRSKVTVAMNMDSSQLGSKDIVKIENRELKPSEVDQIALIAPRATINIVRDYKIVEKAKVRL
> Q9WVI4^.^513^667^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase catalytic domain^PSIBLAST^113.00^0.000e+00^2.000e-25
RKFDDVTMLFSDIVGFTAICAQCTPMQVISMLNELYTRFDHQCGFLDIYKVETIGDAYCVASGLHRKSLCHAKPIALMALKMMELSEEVLTPDGRPIQMRIGIHSGSVLAGVVGVRMPRYCLFGNNVTLASKFESGSHPRRINISPTTYQLLKRE
> Q9ERL9^.^475^626^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase catalytic domain^PSIBLAST^101.00^0.000e+00^9.000e-22
KKFSEVTMLFSDIVGFTAICSQCSPLQVITMLNALYTRFDQQCGELDVYKVETIGDAYCVAGGLHRESDTHAVQIALMALKMMELSNEVMSPHGEPIKMRIGLHSGSVFAGVVGVKMPRYCLFGNNVTLANKFESCSVPRKINVSPTTYRLL
</pre>
</table>
-->
<!-- DATA FILES
Any data files used (e.g. translation table file, substitution matrix
etc. This includes example data file formats if they are not obvious.
For a standard description of what data files are and how embossdata can
be used to inspect and retrieve them, use:
#include file="inc/localfiles.ihtml"
-->
<a name="5.0"></a>
<br><br><br><H2> 5.0 DATA FILES </H2>
None.
<!-- USAGE
Example usage, as run from the command-line.
Many examples illustrating different behaviours is good.
-->
<a name="6.0"></a>
<br><br><br><H2> 6.0 USAGE </H2>
<H3> 6.1 COMMAND LINE ARGUMENTS </H3>
<pre>
Remove ambiguous classified sequences from DHF files.
Version: EMBOSS:6.6.0.0
Standard (Mandatory) qualifiers (* if not always prompted):
[-dhfindir] directory [./] This option specifies the location of
DHF files (domain hits files) (input). A
'domain hits file' contains database hits
(sequences) with domain classification
information, in the DHF format (FASTA or
EMBL-like). The hits are relatives to a SCOP
or CATH family and are found from a search
of a sequence database. Files containing
hits retrieved by PSIBLAST are generated by
using SEQSEARCH.
-overlap integer [10] This option specifies the number of
overlapping residues required for merging of
two hits. Each family is also processed so
that ovlerapping hits (hits with identical
accesssion number that overlap by at least a
user-defined number of residues) are
replaced by a hit that is produced from
merging the two overlapping hits. (Any
integer value)
-dofamilies toggle [N] This option specifies to write a domain
families file. If this option is set a
domain families file is written.
-doambiguities toggle [N] This option specifies whether to write a
domain ambiguities file. If this option is
set a domain ambiguities file is written.
[-dhfoutdir] outdir [./] This option specifies the location of
DHF files (domain hits files) (output). A
'domain hits file' contains database hits
(sequences) with domain classification
information, in the DHF format (FASTA or
EMBL-like). The hits are relatives to a SCOP
or CATH family and are found from a search
of a sequence database. Files containing
hits retrieved by PSIBLAST are generated by
using SEQSEARCH.
* -hitsfile outfile [fam.dhf] This option specifies the name of
domain families file (output). A 'domain
families file' contains sequence relatives
(hits) for each of a number of different
SCOP or CATH families found from searching a
sequence database, e.g. by using SEQSEARCH
(psiblast). The file contains the collated
search results for the indvidual families;
only those hits of unambiguous family
assignment are included. Hits of ambiguous
family assignment are assigned as relatives
to a SCOP or CATH superfamily or fold
instead and are collated into a 'domain
ambiguities file'. The domain families and
ambiguities files are generated by using
SEQSORT and use the same format as a DHF
file (domain hits file).
* -ambigfile outfile [oth.dhf] This option specifies the name of
domain ambiguities file (output). A 'domain
families file' contains sequence relatives
(hits) for each of a number of different
SCOP or CATH families found from searching a
sequence database, e.g. by using SEQSEARCH
(psiblast). The file contains the collated
search results for the indvidual families;
only those hits of unambiguous family
assignment are included. Hits of ambiguous
family assignment are assigned as relatives
to a SCOP or CATH superfamily or fold
instead and are collated into a 'domain
ambiguities file'. The domain families and
ambiguities files are generated by using
SEQSORT and use the same format as a DHF
file (domain hits file).
Additional (Optional) qualifiers: (none)
Advanced (Unprompted) qualifiers: (none)
Associated qualifiers:
"-dhfindir" associated qualifiers
-extension1 string Default file extension
"-dhfoutdir" associated qualifiers
-extension2 string Default file extension
"-hitsfile" associated qualifiers
-odirectory string Output directory
"-ambigfile" associated qualifiers
-odirectory 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
</pre>
</td></tr></table>
<P>
<table border cellspacing=0 cellpadding=3 bgcolor="#ccccff">
<tr bgcolor="#FFFFCC">
<th align="left">Qualifier</th>
<th align="left">Type</th>
<th align="left">Description</th>
<th align="left">Allowed values</th>
<th align="left">Default</th>
</tr>
<tr bgcolor="#FFFFCC">
<th align="left" colspan=5>Standard (Mandatory) qualifiers</th>
</tr>
<tr bgcolor="#FFFFCC">
<td>[-dhfindir]<br>(Parameter 1)</td>
<td>directory</td>
<td>This option specifies the location of DHF files (domain hits files) (input). A 'domain hits file' contains database hits (sequences) with domain classification information, in the DHF format (FASTA or EMBL-like). The hits are relatives to a SCOP or CATH family and are found from a search of a sequence database. Files containing hits retrieved by PSIBLAST are generated by using SEQSEARCH.</td>
<td>Directory</td>
<td>./</td>
</tr>
<tr bgcolor="#FFFFCC">
<td>-overlap</td>
<td>integer</td>
<td>This option specifies the number of overlapping residues required for merging of two hits. Each family is also processed so that ovlerapping hits (hits with identical accesssion number that overlap by at least a user-defined number of residues) are replaced by a hit that is produced from merging the two overlapping hits.</td>
<td>Any integer value</td>
<td>10</td>
</tr>
<tr bgcolor="#FFFFCC">
<td>-dofamilies</td>
<td>toggle</td>
<td>This option specifies to write a domain families file. If this option is set a domain families file is written.</td>
<td>Toggle value Yes/No</td>
<td>No</td>
</tr>
<tr bgcolor="#FFFFCC">
<td>-doambiguities</td>
<td>toggle</td>
<td>This option specifies whether to write a domain ambiguities file. If this option is set a domain ambiguities file is written.</td>
<td>Toggle value Yes/No</td>
<td>No</td>
</tr>
<tr bgcolor="#FFFFCC">
<td>[-dhfoutdir]<br>(Parameter 2)</td>
<td>outdir</td>
<td>This option specifies the location of DHF files (domain hits files) (output). A 'domain hits file' contains database hits (sequences) with domain classification information, in the DHF format (FASTA or EMBL-like). The hits are relatives to a SCOP or CATH family and are found from a search of a sequence database. Files containing hits retrieved by PSIBLAST are generated by using SEQSEARCH.</td>
<td>Output directory</td>
<td>./</td>
</tr>
<tr bgcolor="#FFFFCC">
<td>-hitsfile</td>
<td>outfile</td>
<td>This option specifies the name of domain families file (output). A 'domain families file' contains sequence relatives (hits) for each of a number of different SCOP or CATH families found from searching a sequence database, e.g. by using SEQSEARCH (psiblast). The file contains the collated search results for the indvidual families; only those hits of unambiguous family assignment are included. Hits of ambiguous family assignment are assigned as relatives to a SCOP or CATH superfamily or fold instead and are collated into a 'domain ambiguities file'. The domain families and ambiguities files are generated by using SEQSORT and use the same format as a DHF file (domain hits file).</td>
<td>Output file</td>
<td>fam.dhf</td>
</tr>
<tr bgcolor="#FFFFCC">
<td>-ambigfile</td>
<td>outfile</td>
<td>This option specifies the name of domain ambiguities file (output). A 'domain families file' contains sequence relatives (hits) for each of a number of different SCOP or CATH families found from searching a sequence database, e.g. by using SEQSEARCH (psiblast). The file contains the collated search results for the indvidual families; only those hits of unambiguous family assignment are included. Hits of ambiguous family assignment are assigned as relatives to a SCOP or CATH superfamily or fold instead and are collated into a 'domain ambiguities file'. The domain families and ambiguities files are generated by using SEQSORT and use the same format as a DHF file (domain hits file).</td>
<td>Output file</td>
<td>oth.dhf</td>
</tr>
<tr bgcolor="#FFFFCC">
<th align="left" colspan=5>Additional (Optional) qualifiers</th>
</tr>
<tr>
<td colspan=5>(none)</td>
</tr>
<tr bgcolor="#FFFFCC">
<th align="left" colspan=5>Advanced (Unprompted) qualifiers</th>
</tr>
<tr>
<td colspan=5>(none)</td>
</tr>
<tr bgcolor="#FFFFCC">
<th align="left" colspan=5>Associated qualifiers</th>
</tr>
<tr bgcolor="#FFFFCC">
<td align="left" colspan=5>"-dhfindir" associated directory qualifiers
</td>
</tr>
<tr bgcolor="#FFFFCC">
<td> -extension1<br>-extension_dhfindir</td>
<td>string</td>
<td>Default file extension</td>
<td>Any string</td>
<td>dhf</td>
</tr>
<tr bgcolor="#FFFFCC">
<td align="left" colspan=5>"-dhfoutdir" associated outdir qualifiers
</td>
</tr>
<tr bgcolor="#FFFFCC">
<td> -extension2<br>-extension_dhfoutdir</td>
<td>string</td>
<td>Default file extension</td>
<td>Any string</td>
<td>dhf</td>
</tr>
<tr bgcolor="#FFFFCC">
<td align="left" colspan=5>"-hitsfile" associated outfile qualifiers
</td>
</tr>
<tr bgcolor="#FFFFCC">
<td> -odirectory</td>
<td>string</td>
<td>Output directory</td>
<td>Any string</td>
<td> </td>
</tr>
<tr bgcolor="#FFFFCC">
<td align="left" colspan=5>"-ambigfile" associated outfile qualifiers
</td>
</tr>
<tr bgcolor="#FFFFCC">
<td> -odirectory</td>
<td>string</td>
<td>Output directory</td>
<td>Any string</td>
<td> </td>
</tr>
<tr bgcolor="#FFFFCC">
<th align="left" colspan=5>General qualifiers</th>
</tr>
<tr bgcolor="#FFFFCC">
<td> -auto</td>
<td>boolean</td>
<td>Turn off prompts</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>
<tr bgcolor="#FFFFCC">
<td> -stdout</td>
<td>boolean</td>
<td>Write first file to standard output</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>
<tr bgcolor="#FFFFCC">
<td> -filter</td>
<td>boolean</td>
<td>Read first file from standard input, write first file to standard output</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>
<tr bgcolor="#FFFFCC">
<td> -options</td>
<td>boolean</td>
<td>Prompt for standard and additional values</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>
<tr bgcolor="#FFFFCC">
<td> -debug</td>
<td>boolean</td>
<td>Write debug output to program.dbg</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>
<tr bgcolor="#FFFFCC">
<td> -verbose</td>
<td>boolean</td>
<td>Report some/full command line options</td>
<td>Boolean value Yes/No</td>
<td>Y</td>
</tr>
<tr bgcolor="#FFFFCC">
<td> -help</td>
<td>boolean</td>
<td>Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>
<tr bgcolor="#FFFFCC">
<td> -warning</td>
<td>boolean</td>
<td>Report warnings</td>
<td>Boolean value Yes/No</td>
<td>Y</td>
</tr>
<tr bgcolor="#FFFFCC">
<td> -error</td>
<td>boolean</td>
<td>Report errors</td>
<td>Boolean value Yes/No</td>
<td>Y</td>
</tr>
<tr bgcolor="#FFFFCC">
<td> -fatal</td>
<td>boolean</td>
<td>Report fatal errors</td>
<td>Boolean value Yes/No</td>
<td>Y</td>
</tr>
<tr bgcolor="#FFFFCC">
<td> -die</td>
<td>boolean</td>
<td>Report dying program messages</td>
<td>Boolean value Yes/No</td>
<td>Y</td>
</tr>
<tr bgcolor="#FFFFCC">
<td> -version</td>
<td>boolean</td>
<td>Report version number and exit</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>
</table>
<H3> 6.2 EXAMPLE SESSION </H3>
An example of interactive use of SEQSORT is shown below.
Here is a sample session with <b>seqsort</b>
<p>
<p>
<table width="90%"><tr><td bgcolor="#CCFFFF"><pre>
% <b>seqsort </b>
Remove ambiguous classified sequences from DHF files.
Domain hits directory [./]: <b>../seqnr-keep/hitsnr</b>
Number of overlapping residues required for merging of two hits. [10]: <b>10</b>
Write domain families file. [N]: <b>Y</b>
Write domain ambiguities file. [N]: <b>Y</b>
Domain hits file output directory [./]: <b></b>
</pre></td></tr></table><p>
<p>
<a href="#output.1">Go to the output files for this example</a><p><p>
<!-- All DHF files (of the file extension .dhf specicied in ACD) in directory /test_data were processed by SEQSORT. DHF output files were written to /test_data/seqsort/seqsort_hits. A shared segment of 10 or more identical was required to class two sequences as overlapping. Domain families and ambiguities files called fam.dhf and oth.dhf respectively were written to /test_data/seqsort. -->
<!-- KNOWN BUGS & WARNINGS
Bugs that have not yet been fixed, easily missued features, problems
and caveats etc. Potentially stupid things the program will let you do.
-->
<a name="7.0"></a>
<br><br><br><H2> 7.0 KNOWN BUGS & WARNINGS </H2>
None.
<!-- NOTES
Important general remarks, including:
Restrictions.
Interesting behaviour.
Useful things you can do with this program.
Future plans.
etc.
-->
<a name="8.0"></a>
<br><br><br><H2> 8.0 NOTES </H2>
None.
<H3> 8.1 GLOSSARY OF FILE TYPES </H3>
<table BORDER CELLSPACING=5 CELLPADDING=5 BGCOLOR="#f5f5ff" >
<tr>
<td><b>FILE TYPE</b></td>
<td><b>FORMAT</b></td>
<td><b>DESCRIPTION</b></td>
<td><b>CREATED BY <b></td>
<td><b>SEE ALSO</b></td>
</tr>
<tr>
<td><b>Domain hits file </b></td>
<td> DHF format (FASTA-like). </td>
<td> Database hits (sequences) with domain classification information. The hits are relatives to a SCOP or CATH family (or other node in the structural hierarchies) and are found from a search of a discriminating element (e.g. a protein signature, hidden Markov model, simple frequency matrix, Gribskov profile or Hennikoff profile) against a sequence database. </td>
<td> <a href="seqsearch.html">SEQSEARCH</a> (hits retrieved by PSIBLAST). <a href="sigscan.html">SIGSCAN</a> (hits retrieved by sparse protein signature). <a href="libscan.html">LIBSCAN</a> (hits retrieved by various types of HMM and profile). </td>
<td> N.A. </td>
</tr>
<tr>
<td><b> Domain families & ambiguities file </b></td>
<td> Contains sequence relatives (hits) for each of a number of different SCOP or CATH families found from PSIBLAST searches of a sequence database. The file contains the collated search results for the indvidual families; only those hits of unambiguous family assignment are included. Hits of ambiguous family assignment are assigned as relatives to a SCOP or CATH superfamily or fold instead and are collated into a 'domain ambiguities file'. </td>
<td> The domain families and ambiguities files are generated by using SEQSORT and use the same format as a DHF file (domain hits file). </td>
<td> N.A. </td>
</tr>
<tr>
<td><b>Domain validation file </b></td>
<td> Contains sequence relatives (hits) for each of a number of different SCOP or CATH families, superfamilies and folds. The file contains the collated results from PSIBLAST searches of a sequence database for the indvidual families; hits of unambiguous family assignment are listed under their respective family, otherwise a hit is assigned as relatives to a superfamily or fold instead. </td>
<td> The domain validation file is generated by using SEQNR and uses the same format as a DHF file (domain hits file). </td>
<td> N.A. </td>
</tr>
</table>
None
<!-- DESCRIPTION
A complete, non-technical, user-level description of the application.
-->
<a name="9.0"></a>
<br><br><br><H2> 9.0 DESCRIPTION </H2>
The results of multiple searches of a sequence database using an homology search tool such as blast may contain overlapping or identical hits, especially where the query sequences are related, for instance, belong to different families but the same superfamily. For certain analyses it is desirable to assign a hit with confidence to a unique family, or otherwise assign it as a member of a larger superfamily or fold instead. SEQSORT reads a directory of DHF files (domain hits files) where each file containing hits to a different SCOP family, compares, processes and collates the hits and writes a directory of DHF files which contain only those hits that could be uniquely assigned to a SCOP family. Optionally, two further files are written: (i) a domain families file, of hits (from ALL the input files) that could be uniquely assigned to a SCOP family and (ii) a domain ambiguities file, for hits (from ALL the input files) of ambiguous family assignment which are assigned as relatives to a SCOP superfamily or fold instead.
<!-- ALGORITHM
A technical description of algorithmic aspects, describing exactly how
the key aspects of the application work.
-->
<a name="10.0"></a>
<br><br><br><H2> 10.0 ALGORITHM </H2>
A rough outline of the algorithm follows; a better description will appear in a publication in preparation. Hits from searches for all domain families are collated into a single list and the list sorted according to family name. The hits hits within each family are sorted by accession number, then hits within a family and with identical accession number are sorted by the start position of the hit relative to the full length sequence in swissprot. In each family identical hits (i.e. those with identical accession number and the same start and end points relative to the full-length sequence in swissprot) were removed leaving only a single copy. Each family is also processed so that ovlerapping hits (hits with identical accesssion number that overlap by at least a user-defined number of residues) are replaced by a hit that is produced from merging the two overlapping hits. If two hits have the same accession number and overlap but are from searches for different families, the hits are merged and the merged hit placed into a new list for hits to superfamilies (if the two families belonged to the same superfamily) or for hits to folds (if the two families were in different superfamilies but the same fold). In this way hits that are unique to a particular family are identified, and hits of ambiguous family assignment are assigned as belonging to a superfamily or fold instead.
<!-- RELATED APPLICATIONS
Other applications that either generate the input, use the output or
are in some other way related to the application are described here.
(Take this from "Sister applications" in the old documentation)
-->
<a name="11.0"></a>
<br><br><br><H2> 11.0 RELATED APPLICATIONS </H2>
<h2><a name="See also">See also</a></h2>
<table border cellpadding=4 bgcolor="#FFFFF0">
<tr><th>Program name</th>
<th>Description</th></tr>
<tr>
<td><a href="../domainatrix/cathparse.html">cathparse</a></td>
<td>Generate DCF file from raw CATH files</td>
</tr>
<tr>
<td><a href="../domalign/domainalign.html">domainalign</a></td>
<td>Generate alignments (DAF file) for nodes in a DCF file</td>
</tr>
<tr>
<td><a href="../domainatrix/domainnr.html">domainnr</a></td>
<td>Remove redundant domains from a DCF file</td>
</tr>
<tr>
<td><a href="../domalign/domainrep.html">domainrep</a></td>
<td>Reorder DCF file to identify representative structures</td>
</tr>
<tr>
<td><a href="../domainatrix/domainseqs.html">domainseqs</a></td>
<td>Add sequence records to a DCF file</td>
</tr>
<tr>
<td><a href="../domainatrix/domainsse.html">domainsse</a></td>
<td>Add secondary structure records to a DCF file</td>
</tr>
<tr>
<td><a href="../../emboss/apps/helixturnhelix.html">helixturnhelix</a></td>
<td>Identify nucleic acid-binding motifs in protein sequences</td>
</tr>
<tr>
<td><a href="../signature/libgen.html">libgen</a></td>
<td>Generate discriminating elements from alignments</td>
</tr>
<tr>
<td><a href="../signature/matgen3d.html">matgen3d</a></td>
<td>Generate a 3D-1D scoring matrix from CCF files</td>
</tr>
<tr>
<td><a href="../../emboss/apps/pepcoil.html">pepcoil</a></td>
<td>Predict coiled coil regions in protein sequences</td>
</tr>
<tr>
<td><a href="../signature/rocon.html">rocon</a></td>
<td>Generate a hits file from comparing two DHF files</td>
</tr>
<tr>
<td><a href="../signature/rocplot.html">rocplot</a></td>
<td>Perform ROC analysis on hits files</td>
</tr>
<tr>
<td><a href="../domainatrix/scopparse.html">scopparse</a></td>
<td>Generate DCF file from raw SCOP files</td>
</tr>
<tr>
<td><a href="../domalign/seqalign.html">seqalign</a></td>
<td>Extend alignments (DAF file) with sequences (DHF file)</td>
</tr>
<tr>
<td><a href="seqfraggle.html">seqfraggle</a></td>
<td>Remove fragment sequences from DHF files</td>
</tr>
<tr>
<td><a href="seqwords.html">seqwords</a></td>
<td>Generate DHF files from keyword search of UniProt</td>
</tr>
<tr>
<td><a href="../domainatrix/ssematch.html">ssematch</a></td>
<td>Search a DCF file for secondary structure matches</td>
</tr>
</table>
<!-- DIAGNOSTIC ERROR MESSAGES
Description of error messages or log file, if one is written.
-->
<a name="12.0"></a>
<br><br><br><H2> 12.0 DIAGNOSTIC ERROR MESSAGES </H2>
None.
<!-- AUTHORS -->
<a name="13.0"><br><br><br><H2> 13.0 AUTHORS </H2></a>
Ranjeeva Ranasinghe
<br><br>
Jon Ison <a href="mailto:jison@ebi.ac.uk">(jison@ebi.ac.uk)</a>
<br>The European Bioinformatics Institute
Wellcome Trust Genome Campus
Cambridge CB10 1SD
UK
<!-- REFERENCES
Quote the paper where the application was first published, described, used etc.
-->
<a name="14.0"></a>
<br><br><br><H2> 14.0 REFERENCES </H2>
Please cite the authors and EMBOSS.
<br><br>
<i>Rice P, Longden I and Bleasby A (2000) "EMBOSS - The European
Molecular Biology Open Software Suite" Trends in Genetics,
15:276-278.
<p>
See also <a href="http://emboss.sourceforge.net/">http://emboss.sourceforge.net/</a></i>
<H3>14.1 Other useful references </H3>
<br>
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</HTML>
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