CSC

 
 
Tehdyt toimenpiteet
EMBOSS
diffseq

 

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Function

Compare and report features of two similar sequences

Description

diffseq reads two sequences which typically are very similar or almost identical. It finds regions of overlap between the two sequences and reports on differences between the features of the two sequences within these regions. The output is a standard EMBOSS report file. The start and end positions of the regions of overlap are reported. Any differences between the sequences, and any features (except the source feature) that overlap those differences, are included in the output report.

The differences are also reported for each input sequence as two separate feature table output files.

Algorithm

diffseq searches for identical matches between all sequence words from both sequences. Identical sequence regions are found by creating a hash table of subsequences of user-defined size (-wordsize option), which is 10 by default. It then reduces the matches to a minimum set of overlapping matches by sorting them in order of size (largest size first). For each such match it removes any smaller matches that overlap. The result is a set of the longest regions of identity between the two sequences that do not overlap with each other. The mismatched regions between these matches are reported.

Usage

Here is a sample session with diffseq 


% diffseq tembl:x65923 tembl:ay411291 
Compare and report features of two similar sequences
Word size [10]: 
Output report [x65923.diffseq]: 
Features output [X65923.diffgff]: 
Second features output [AY411291.diffgff]:

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

Command line arguments 

Compare and report features of two similar sequences
Version: EMBOSS:6.4.0.0

   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 (default
                                  -rformat diffseq)
  [-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
   -rstrandshow3       boolean    Show the nucleotide strand 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 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

Qualifier Type Description Allowed values Default
Standard (Mandatory) qualifiers
[-asequence]
(Parameter 1)		 sequence Sequence filename and optional format, or reference (input USA) Readable sequence Required
[-bsequence]
(Parameter 2)		 sequence Sequence filename and optional format, or reference (input USA) Readable sequence Required
-wordsize integer 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 10
[-outfile]
(Parameter 3)		 report Output report file name (default -rformat diffseq) <*>.diffseq
[-aoutfeat]
(Parameter 4)		 featout File for output of first sequence's features Writeable feature table $(asequence.name).diffgff
[-boutfeat]
(Parameter 5)		 featout File for output of second sequence's features Writeable feature table $(bsequence.name).diffgff
Additional (Optional) qualifiers
-globaldifferences boolean 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. Boolean value Yes/No No
Advanced (Unprompted) qualifiers
(none)
Associated qualifiers
"-asequence" associated sequence qualifiers
-sbegin1
-sbegin_asequence		 integer Start of the sequence to be used Any integer value 0
-send1
-send_asequence		 integer End of the sequence to be used Any integer value 0
-sreverse1
-sreverse_asequence		 boolean Reverse (if DNA) Boolean value Yes/No N
-sask1
-sask_asequence		 boolean Ask for begin/end/reverse Boolean value Yes/No N
-snucleotide1
-snucleotide_asequence		 boolean Sequence is nucleotide Boolean value Yes/No N
-sprotein1
-sprotein_asequence		 boolean Sequence is protein Boolean value Yes/No N
-slower1
-slower_asequence		 boolean Make lower case Boolean value Yes/No N
-supper1
-supper_asequence		 boolean Make upper case Boolean value Yes/No N
-sformat1
-sformat_asequence		 string Input sequence format Any string  
-sdbname1
-sdbname_asequence		 string Database name Any string  
-sid1
-sid_asequence		 string Entryname Any string  
-ufo1
-ufo_asequence		 string UFO features Any string  
-fformat1
-fformat_asequence		 string Features format Any string  
-fopenfile1
-fopenfile_asequence		 string Features file name Any string  
"-bsequence" associated sequence qualifiers
-sbegin2
-sbegin_bsequence		 integer Start of the sequence to be used Any integer value 0
-send2
-send_bsequence		 integer End of the sequence to be used Any integer value 0
-sreverse2
-sreverse_bsequence		 boolean Reverse (if DNA) Boolean value Yes/No N
-sask2
-sask_bsequence		 boolean Ask for begin/end/reverse Boolean value Yes/No N
-snucleotide2
-snucleotide_bsequence		 boolean Sequence is nucleotide Boolean value Yes/No N
-sprotein2
-sprotein_bsequence		 boolean Sequence is protein Boolean value Yes/No N
-slower2
-slower_bsequence		 boolean Make lower case Boolean value Yes/No N
-supper2
-supper_bsequence		 boolean Make upper case Boolean value Yes/No N
-sformat2
-sformat_bsequence		 string Input sequence format Any string  
-sdbname2
-sdbname_bsequence		 string Database name Any string  
-sid2
-sid_bsequence		 string Entryname Any string  
-ufo2
-ufo_bsequence		 string UFO features Any string  
-fformat2
-fformat_bsequence		 string Features format Any string  
-fopenfile2
-fopenfile_bsequence		 string Features file name Any string  
"-outfile" associated report qualifiers
-rformat3
-rformat_outfile		 string Report format Any string diffseq
-rname3
-rname_outfile		 string Base file name Any string  
-rextension3
-rextension_outfile		 string File name extension Any string  
-rdirectory3
-rdirectory_outfile		 string Output directory Any string  
-raccshow3
-raccshow_outfile		 boolean Show accession number in the report Boolean value Yes/No N
-rdesshow3
-rdesshow_outfile		 boolean Show description in the report Boolean value Yes/No N
-rscoreshow3
-rscoreshow_outfile		 boolean Show the score in the report Boolean value Yes/No Y
-rstrandshow3
-rstrandshow_outfile		 boolean Show the nucleotide strand in the report Boolean value Yes/No Y
-rusashow3
-rusashow_outfile		 boolean Show the full USA in the report Boolean value Yes/No N
-rmaxall3
-rmaxall_outfile		 integer Maximum total hits to report Any integer value 0
-rmaxseq3
-rmaxseq_outfile		 integer Maximum hits to report for one sequence Any integer value 0
"-aoutfeat" associated featout qualifiers
-offormat4
-offormat_aoutfeat		 string Output feature format Any string  
-ofopenfile4
-ofopenfile_aoutfeat		 string Features file name Any string  
-ofextension4
-ofextension_aoutfeat		 string File name extension Any string  
-ofdirectory4
-ofdirectory_aoutfeat		 string Output directory Any string  
-ofname4
-ofname_aoutfeat		 string Base file name Any string  
-ofsingle4
-ofsingle_aoutfeat		 boolean Separate file for each entry Boolean value Yes/No N
"-boutfeat" associated featout qualifiers
-offormat5
-offormat_boutfeat		 string Output feature format Any string  
-ofopenfile5
-ofopenfile_boutfeat		 string Features file name Any string  
-ofextension5
-ofextension_boutfeat		 string File name extension Any string  
-ofdirectory5
-ofdirectory_boutfeat		 string Output directory Any string  
-ofname5
-ofname_boutfeat		 string Base file name Any string  
-ofsingle5
-ofsingle_boutfeat		 boolean Separate file for each entry Boolean value Yes/No N
General qualifiers
-auto boolean Turn off prompts Boolean value Yes/No N
-stdout boolean Write first file to standard output Boolean value Yes/No N
-filter boolean Read first file from standard input, write first file to standard output Boolean value Yes/No N
-options boolean Prompt for standard and additional values Boolean value Yes/No N
-debug boolean Write debug output to program.dbg Boolean value Yes/No N
-verbose boolean Report some/full command line options Boolean value Yes/No Y
-help boolean Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose Boolean value Yes/No N
-warning boolean Report warnings Boolean value Yes/No Y
-error boolean Report errors Boolean value Yes/No Y
-fatal boolean Report fatal errors Boolean value Yes/No Y
-die boolean Report dying program messages Boolean value Yes/No Y
-version boolean Report version number and exit Boolean value Yes/No N

Input file format

This program reads in two 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 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 sequence 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="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="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
//

Database entry: tembl:ay411291

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
//

Output file format

The output is a standard EMBOSS report file.

The results can be output in one of several styles by using the command-line qualifier -rformat 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, draw, restrict, excel, feattable, motif, nametable, regions, seqtable, simple, srs, table, tagseq.

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

By default diffseq writes a 'diffseq' report file.

Output files for usage example

File: x65923.diffseq

########################################
# Program: diffseq
# Rundate: Fri 15 Jul 2011 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='InterPro:IPR000626' db_xref='InterPro:IPR006846' db_xref='InterPro:IPR019954' db_xref='InterPro:IPR019955' db_xref='InterPro:IPR019956' 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: 2
# Total_length: 920
# Reported_sequences: 1
# Reported_hitcount: 1
#---------------------------------------

File: AY411291.diffgff

##gff-version 3
##sequence-region AY411291 1 402
#!Date 2011-07-15
#!Type DNA
#!Source-version EMBOSS 6.4.0.0
AY411291	diffseq	sequence_conflict	228	228	1.000	+	.	ID=AY411291.1;note=SNP in X65923;replace=t

File: X65923.diffgff

##gff-version 3
##sequence-region X65923 1 518
#!Date 2011-07-15
#!Type DNA
#!Source-version EMBOSS 6.4.0.0
X65923	diffseq	sequence_conflict	284	284	1.000	+	.	ID=X65923.1;note=SNP in AY411291;replace=c

The first line is the title giving the names of the sequences used.

The next two non-blank lines state the positions in each sequence where the detected overlap between them starts.

There then follows a set of reports of the mismatches between the sequences.
Each report consists of 4 or more lines.

  • 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.
  • 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.
  • Next is a line starting "Sequence:" giving the sequence of the mismatch in the first sequence.

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.

At the end of the report are two non-blank lines giving the positions in each sequence where the detected overlap between them ends.

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).

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.

It should be noted that not all features are reported.

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.

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.

Data files

None

Notes

diffseq is useful when looking for SNPs, differences between strains of an organism and anything else that requires the differences between two eseentially identical sequences to be highlighted.

Identical sequence regions are found by creating a hash table of subsequences of user-defined size (-wordsize option, which is 10 by default). Making this value larger (e.g. 20) may speed-up the program slightly, but will mean that any two differences within wordsize bases bases or residues of each other will be grouped as a single region of difference. This value may be made smaller to improve the resolution of nearby differences, but the program will go much slower.

The sequences can be very long; it should be possible to find differences between sequences that are Mega-bases long. If, however, you run out of memory, use a larger word size. This 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.

By default, diffseq finds regions of identity that are at least as long as the specified word-size. This is what is typically required when working with long overlapping nucleic acid sequences, where the non-overlapping sequence ends are less interesting. If however, you have protein sequences or short RNA sequences then you may well be interested in differences at the very ends. The -globaldifferences option when set means the differences at the ends will also be reported.

References

None.

Warnings

None.

Diagnostic Error Messages

None.

Exit status

It always exits with status 0.

Known bugs

None.

See also

Program name Description

Author(s)

Gary Williams formerly at:
MRC Rosalind Franklin Centre for Genomics Research Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SB, UK

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

History

Written 15th Aug 2000 - Gary Williams.

18th Aug 2000 - Added writing out GFF files of the mismatched regions

Target users

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

Comments

None