                                   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:6.2.0

   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
  [-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


Input file format

   This program reads in two nucleic acid sequence USAs or two protein
   sequence USAs.

  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:P62861"
FT                   /db_xref="HGNC:3597"
FT                   /db_xref="HSSP:1GJZ"
FT                   /db_xref="InterPro:IPR006846"
FT                   /db_xref="UniProtKB/Swiss-Prot:P35544"
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, trace, listfile, dbmotif, diffseq, excel,
   feattable, motif, 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 Jan 2010 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:P62861' db_xref
='HGNC:3597' db_xref='HSSP:1GJZ' db_xref='InterPro:IPR006846' db_xref='UniProtKB
/Swiss-Prot:P35544' 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 2010-01-15
#!Type DNA
#!Source-version EMBOSS 6.2.0
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 2010-01-15
#!Type DNA
#!Source-version EMBOSS 6.2.0
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 (gwilliam (c) rfcgr.mrc.ac.uk)
   MRC Rosalind Franklin Centre for Genomics Research Wellcome Trust
   Genome Campus, Hinxton, Cambridge, CB10 1SB, UK

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
