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diffseq.html
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<HTML>
<HEAD>
<TITLE>
EMBOSS
</TITLE>
</HEAD>
<BODY BGCOLOR="#FFFFFF" text="#000000">
<table align=center border=0 cellspacing=0 cellpadding=0>
<tr><td valign=top>
<A HREF="/" ONMOUSEOVER="self.status='Go to the EMBOSS home page';return true"><img border=0 src="emboss_icon.jpg" alt="" width=150 height=48></a>
</td>
<td align=left valign=middle>
<b><font size="+6">
diffseq
</font></b>
</td></tr>
</table>
<br>
<p>
<H2>
Function
</H2>
Find differences between nearly identical sequences
<H2>
Description
</H2>
<b>diffseq</b> takes two overlapping, nearly identical sequences and
reports the differences between them, together with any features that
overlap with these regions. GFF files of the differences in each
sequence are also produced.
<p>
<b>diffseq</b> finds the region of overlap of the input sequences and
then reports differences within this region, like a local alignment.
<p>
The start and end positions of the overlap are reported.
<p>
<b>diffseq</b> should be of value when looking for SNPs, differences
between strains of an organism and anything else that requires the
differences between sequences to be highlighted.
<p>
The sequences can be very long. The program does a match of all
sequence words of size 10 (by default). It then reduces this to the
minimum set of overlapping matches by sorting the matches in order of
size (largest size first) and then for each such match it removes any
smaller matches that overlap. The result is a set of the longest
ungapped alignments between the two sequences that do not overlap with
each other. The mismatched regions between these matches are reported.
<p>
It should be possible to find differences between sequences that are Mega-bases
long.
<H2>
Usage
</H2>
<b>Here is a sample session with diffseq</b>
<p>
<p>
<table width="90%"><tr><td bgcolor="#CCFFFF"><pre>
% <b>diffseq tembl:x65923 tembl:ay411291 </b>
Find differences between nearly identical sequences
Word size [10]: <b></b>
Output report [x65923.diffseq]: <b></b>
Features output [X65923.diffgff]: <b></b>
Second features output [AY411291.diffgff]: <b></b>
</pre></td></tr></table><p>
<p>
<a href="#input.1">Go to the input files for this example</a><br><a href="#output.1">Go to the output files for this example</a><p><p>
<H2>
Command line arguments
</H2>
<table CELLSPACING=0 CELLPADDING=3 BGCOLOR="#f5f5ff" ><tr><td>
<pre>
Standard (Mandatory) qualifiers:
[-asequence] sequence Sequence filename and optional format, or
reference (input USA)
[-bsequence] sequence Sequence filename and optional format, or
reference (input USA)
-wordsize integer [10] The similar regions between the two
sequences are found by creating a hash table
of 'wordsize'd subsequences. 10 is a
reasonable default. Making this value larger
(20?) may speed up the program slightly,
but will mean that any two differences
within 'wordsize' of each other will be
grouped as a single region of difference.
This value may be made smaller (4?) to
improve the resolution of nearby
differences, but the program will go much
slower. (Integer 2 or more)
[-outfile] report [*.diffseq] Output report file name
[-aoutfeat] featout [$(asequence.name).diffgff] File for output
of first sequence's features
[-boutfeat] featout [$(bsequence.name).diffgff] File for output
of second sequence's features
Additional (Optional) qualifiers:
-globaldifferences boolean [N] Normally this program will find regions
of identity that are the length of the
specified word-size or greater and will then
report the regions of difference between
these matching regions. This works well and
is what most people want if they are working
with long overlapping nucleic acid
sequences. You are usually not interested in
the non-overlapping ends of these
sequences. If you have protein sequences or
short RNA sequences however, you will be
interested in differences at the very ends .
It this option is set to be true then the
differences at the ends will also be
reported.
Advanced (Unprompted) qualifiers: (none)
Associated qualifiers:
"-asequence" associated qualifiers
-sbegin1 integer Start of the sequence to be used
-send1 integer End of the 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
"-bsequence" associated qualifiers
-sbegin2 integer Start of the sequence to be used
-send2 integer End of the sequence to be used
-sreverse2 boolean Reverse (if DNA)
-sask2 boolean Ask for begin/end/reverse
-snucleotide2 boolean Sequence is nucleotide
-sprotein2 boolean Sequence is protein
-slower2 boolean Make lower case
-supper2 boolean Make upper case
-sformat2 string Input sequence format
-sdbname2 string Database name
-sid2 string Entryname
-ufo2 string UFO features
-fformat2 string Features format
-fopenfile2 string Features file name
"-outfile" associated qualifiers
-rformat3 string Report format
-rname3 string Base file name
-rextension3 string File name extension
-rdirectory3 string Output directory
-raccshow3 boolean Show accession number in the report
-rdesshow3 boolean Show description in the report
-rscoreshow3 boolean Show the score in the report
-rusashow3 boolean Show the full USA in the report
-rmaxall3 integer Maximum total hits to report
-rmaxseq3 integer Maximum hits to report for one sequence
"-aoutfeat" associated qualifiers
-offormat4 string Output feature format
-ofopenfile4 string Features file name
-ofextension4 string File name extension
-ofdirectory4 string Output directory
-ofname4 string Base file name
-ofsingle4 boolean Separate file for each entry
"-boutfeat" associated qualifiers
-offormat5 string Output feature format
-ofopenfile5 string Features file name
-ofextension5 string File name extension
-ofdirectory5 string Output directory
-ofname5 string Base file name
-ofsingle5 boolean Separate file for each entry
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
</pre>
</td></tr></table>
<P>
<table border cellspacing=0 cellpadding=3 bgcolor="#ccccff">
<tr bgcolor="#FFFFCC">
<th align="left" colspan=2>Standard (Mandatory) qualifiers</th>
<th align="left">Allowed values</th>
<th align="left">Default</th>
</tr>
<tr>
<td>[-asequence]<br>(Parameter 1)</td>
<td>Sequence filename and optional format, or reference (input USA)</td>
<td>Readable sequence</td>
<td><b>Required</b></td>
</tr>
<tr>
<td>[-bsequence]<br>(Parameter 2)</td>
<td>Sequence filename and optional format, or reference (input USA)</td>
<td>Readable sequence</td>
<td><b>Required</b></td>
</tr>
<tr>
<td>-wordsize</td>
<td>The similar regions between the two sequences are found by creating a hash table of 'wordsize'd subsequences. 10 is a reasonable default. Making this value larger (20?) may speed up the program slightly, but will mean that any two differences within 'wordsize' of each other will be grouped as a single region of difference. This value may be made smaller (4?) to improve the resolution of nearby differences, but the program will go much slower.</td>
<td>Integer 2 or more</td>
<td>10</td>
</tr>
<tr>
<td>[-outfile]<br>(Parameter 3)</td>
<td>Output report file name</td>
<td>Report output file</td>
<td><i><*></i>.diffseq</td>
</tr>
<tr>
<td>[-aoutfeat]<br>(Parameter 4)</td>
<td>File for output of first sequence's features</td>
<td>Writeable feature table</td>
<td>$(asequence.name).diffgff</td>
</tr>
<tr>
<td>[-boutfeat]<br>(Parameter 5)</td>
<td>File for output of second sequence's features</td>
<td>Writeable feature table</td>
<td>$(bsequence.name).diffgff</td>
</tr>
<tr bgcolor="#FFFFCC">
<th align="left" colspan=2>Additional (Optional) qualifiers</th>
<th align="left">Allowed values</th>
<th align="left">Default</th>
</tr>
<tr>
<td>-globaldifferences</td>
<td>Normally this program will find regions of identity that are the length of the specified word-size or greater and will then report the regions of difference between these matching regions. This works well and is what most people want if they are working with long overlapping nucleic acid sequences. You are usually not interested in the non-overlapping ends of these sequences. If you have protein sequences or short RNA sequences however, you will be interested in differences at the very ends . It this option is set to be true then the differences at the ends will also be reported.</td>
<td>Boolean value Yes/No</td>
<td>No</td>
</tr>
<tr bgcolor="#FFFFCC">
<th align="left" colspan=2>Advanced (Unprompted) qualifiers</th>
<th align="left">Allowed values</th>
<th align="left">Default</th>
</tr>
<tr>
<td colspan=4>(none)</td>
</tr>
</table>
<H2>
Input file format
</H2>
This program reads in two nucleic acid sequence USAs or two protein
sequence USAs.
<p>
<a name="input.1"></a>
<h3>Input files for usage example </h3>
'tembl:x65923' is a sequence entry in the example nucleic acid database 'tembl'
<p>
<p><h3>Database entry: tembl:x65923</h3>
<table width="90%"><tr><td bgcolor="#FFCCFF">
<pre>
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 EMBL/GenBank/DDBJ databases.
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 sequences in the Finkel-Biskis-Reilly murine sarcoma virus";
RL Oncogene 8(9):2537-2546(1993).
XX
DR H-InvDB; HIT000322806.
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="HGNC:3597"
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
//
</pre>
</td></tr></table><p>
<p><h3>Database entry: tembl:ay411291</h3>
<table width="90%"><tr><td bgcolor="#FFCCFF">
<pre>
ID AY411291; SV 1; linear; genomic DNA; GSS; HUM; 402 BP.
XX
AC AY411291;
XX
DT 13-DEC-2003 (Rel. 78, Created)
DT 17-DEC-2003 (Rel. 78, Last updated, Version 2)
XX
DE Homo sapiens FAU gene, VIRTUAL TRANSCRIPT, partial sequence, genomic survey
DE sequence.
XX
KW GSS.
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 1-402
RX DOI; 10.1126/science.1088821.
RX PUBMED; 14671302.
RA Clark A.G., Glanowski S., Nielson R., Thomas P., Kejariwal A., Todd M.A.,
RA Tanenbaum D.M., Civello D.R., Lu F., Murphy B., Ferriera S., Wang G.,
RA Zheng X.H., White T.J., Sninsky J.J., Adams M.D., Cargill M.;
RT "Inferring nonneutral evolution from human-chimp-mouse orthologous gene
RT trios";
RL Science 302(5652):1960-1963(2003).
XX
RN [2]
RP 1-402
RA Clark A.G., Glanowski S., Nielson R., Thomas P., Kejariwal A., Todd M.A.,
RA Tanenbaum D.M., Civello D.R., Lu F., Murphy B., Ferriera S., Wang G.,
RA Zheng X.H., White T.J., Sninsky J.J., Adams M.D., Cargill M.;
RT ;
RL Submitted (16-NOV-2003) to the EMBL/GenBank/DDBJ databases.
RL Celera Genomics, 45 West Gude Drive, Rockville, MD 20850, USA
XX
CC This sequence was made by sequencing genomic exons and ordering
CC them based on alignment.
XX
FH Key Location/Qualifiers
FH
FT source 1..402
FT /organism="Homo sapiens"
FT /mol_type="genomic DNA"
FT /db_xref="taxon:9606"
FT gene <1..>402
FT /gene="FAU"
FT /locus_tag="HCM4175"
XX
SQ Sequence 402 BP; 95 A; 110 C; 129 G; 68 T; 0 other;
atgcagctct ttgtccgcgc ccaggagcta cacaccttcg aggtgaccgg ccaggaaacg 60
gtcgcccaga tcaaggctca tgtagcctca ctggagggca ttgccccgga agatcaagtc 120
gtgctcctgg caggcgcgcc cctggaggat gaggccactc tgggccagtg cggggtggag 180
gccctgacta ccctggaagt agcaggccgc atgcttggag gtaaagtcca tggttccctg 240
gcccgtgctg gaaaagtgag aggtcagact cctaaggtgg ccaaacagga gaagaagaag 300
aagaagacag gtcgggctaa gcggcggatg cagtacaacc ggcgctttgt caacgttgtg 360
cccacctttg gcaagaagaa gggccccaat gccaactctt aa 402
//
</pre>
</td></tr></table><p>
<H2>
Output file format
</H2>
<p>
The output is a standard EMBOSS report file.
<p>
The results can be output in one of several styles by using the
command-line qualifier <b>-rformat xxx</b>, where 'xxx' is replaced by
the name of the required format. The available format names are: embl,
genbank, gff, pir, swiss, trace, listfile, dbmotif, diffseq, excel,
feattable, motif, regions, seqtable, simple, srs, table, tagseq
<p>
See:
<A href="http://emboss.sf.net/docs/themes/ReportFormats.html">
http://emboss.sf.net/docs/themes/ReportFormats.html</A>
for further information on report formats.
<p>
<p>
By default <b>diffseq</b> writes a 'diffseq' report file.
<p>
<a name="output.1"></a>
<h3>Output files for usage example </h3>
<p><h3>File: x65923.diffseq</h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
########################################
# Program: diffseq
# Rundate: Sun 15 Jul 2007 12:00:00
# Commandline: diffseq
# [-asequence] tembl:x65923
# [-bsequence] tembl:ay411291
# Report_format: diffseq
# Report_file: x65923.diffseq
# Additional_files: 2
# 1: X65923.diffgff (Feature file for first sequence)
# 2: AY411291.diffgff (Feature file for second sequence)
########################################
#=======================================
#
# Sequence: X65923 from: 1 to: 518
# HitCount: 1
#
# Compare: AY411291 from: 1 to: 402
#
# X65923 overlap starts at 57
# AY411291 overlap starts at 1
#
#
#=======================================
X65923 284-284 Length: 1
Feature: CDS 57-458 gene='fau' db_xref='GDB:135476' db_xref='GOA:P35544' db_xref='GOA:P62861' db_xref='HGNC:3597' db_xref='UniProtKB/Swiss-Prot:P35544' db_xref='UniProtKB/Swiss-Prot:P62861' protein_id='CAA46716.1'
Feature: misc_feature 279-458 note='S30 part'
Sequence: t
Sequence: c
Feature: gene 1-402 gene='FAU' locus_tag='HCM4175'
AY411291 228-228 Length: 1
#---------------------------------------
#
# Overlap_end: 458 in X65923
# Overlap_end: 402 in AY411291
#
# SNP_count: 1
# Transitions: 1
# Transversions: 0
#
#---------------------------------------
#---------------------------------------
# Total_sequences: 1
# Total_hitcount: 1
#---------------------------------------
</pre>
</td></tr></table><p>
<p><h3>File: AY411291.diffgff</h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
##gff-version 2.0
##date 2006-07-15
##Type DNA AY411291
AY411291 diffseq conflict 228 228 1.000 + . Sequence "AY411291.1" ; note "SNP in X65923" ; replace "t"
</pre>
</td></tr></table><p>
<p><h3>File: X65923.diffgff</h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
##gff-version 2.0
##date 2006-07-15
##Type DNA X65923
X65923 diffseq conflict 284 284 1.000 + . Sequence "X65923.1" ; note "SNP in AY411291" ; replace "c"
</pre>
</td></tr></table><p>
<p>
The first line is the title giving the names of the sequences used.
<p>
The next two non-blank lines state the positions in each sequence
where the detected overlap between them starts.
<p>
There then follows a set of reports of the mismatches between the sequences.
<br>
Each report consists of 4 or more lines.
<br>
<ul>
<li>The first line has the name of the first sequence followed by the
start and end positions of the mismatched region in that sequence,
followed by the length of the mismatched region. If the mismatched
region is of zero length in this sequence, then only the position of
the last matching base before the mismatch is given.</li>
<li>If a feature of the first sequence overlaps with this mismatch
region, then one or more lines starting with 'Feature:' comes next
with the type, position and tag field of the feature.</li>
<li>Next is a line starting "Sequence:" giving the sequence of the
mismatch in the first sequence.</li> </ul>
<p>
This is followed by the equivalent information for the second
sequence, but in the reverse order, namely 'Sequence:' line,
'Feature:' lines and line giving the position of the mismatch in the
second sequence.
<p>
At the end of the report are two non-blank lines giving the positions in each
sequence where the detected
overlap between them ends.
<p>
The last three lines of the report gives the counts of SNPs (defined
as a change of one nucleotide to one other nucleotide, no deletions or
insertions are counted, no multi-base changes are counted).
<p>
If the input sequences are nucleic acid, The counts of transitions
(Pyrimide to Pyrimidine or Purine to Purine) and transversions
(Pyrimidine to Purine) are also given.
<p>
It should be noted that not all features are reported.
<p>
The 'source' feature found in all EMBL/Genbank feature table entries is
not reported as this covers all of the sequence and so overlaps with any
difference found in that sequence and so is uninformative and
irritating. It has therefore been removed from the output report.
<p>
The translation information of CDS features is often extremely long and
does not add useful information to the report. It has therefore been
removed from the output report.
<H2>
Data files
</H2>
None
<H2>
Notes
</H2>
It should be noted that not all features are reported.
<p>
The 'source' feature found in all EMBL/Genbank feature table entries is
not reported as this covers all of the sequence and so overlaps with any
difference found in that sequence and so is uninformative and
irritating. It has therefore been removed from the output report.
<p>
The translation information of CDS features is often extremely long and
does not add useful information to the report. It has therefore been
removed from the output report.
<p>
If you run out of memory, use a larger word size.
<p>
Using a larger word size increases the length between mismatches that
will be reported as one event. Thus a word size of 50 will report two
single-base differences that are with 50 bases of each other as one mismatch.
<H2>
References
</H2>
None.
<H2>
Warnings
</H2>
None.
<H2>
Diagnostic Error Messages
</H2>
None.
<H2>
Exit status
</H2>
It always exits with status 0.
<H2>
Known bugs
</H2>
None.
<h2><a name="See also">See also</a></h2>
<table border cellpadding=4 bgcolor="#FFFFF0">
<tr><th>Program name</th><th>Description</th></tr>
</table>
<H2>
Author(s)
</H2>
Gary Williams (gwilliam © rfcgr.mrc.ac.uk)
<br>
MRC Rosalind Franklin Centre for Genomics Research
Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SB, UK
<H2>
History
</H2>
Written 15th Aug 2000 - Gary Williams.
<p>
18th Aug 2000 - Added writing out GFF files of the mismatched regions
<H2>
Target users
</H2>
This program is intended to be used by everyone and everything, from naive users to embedded scripts.
<H2>
Comments
</H2>
None
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