
ALLVERSUSALL documentation

CONTENTS

   1.0 SUMMARY 
   2.0 INPUTS & OUTPUTS 
   3.0 INPUT FILE FORMAT 
   4.0 OUTPUT FILE FORMAT 
   5.0 DATA FILES 
   6.0 USAGE 
   7.0 KNOWN BUGS & WARNINGS 
   8.0 NOTES 
   9.0 DESCRIPTION 
   10.0 ALGORITHM 
   11.0 RELATED APPLICATIONS 
   12.0 DIAGNOSTIC ERROR MESSAGES 
   13.0 AUTHORS 
   14.0 REFERENCES 

1.0 SUMMARY

   Does an all-versus-all global alignment for each set of sequences in
   an input directory and writes files of sequence similarity values

2.0 INPUTS & OUTPUTS

   ALLVERSUSALL reads a directory of files each containing a set of 2 or
   more sequences, performs an all-versus-all global alignment on each
   set and writes a file of sequence similarity values for each input
   file. The output files have the same base name as the input files. The
   path and extension of the input and output files are specified by the
   user in the ACD file.

3.0 INPUT FILE FORMAT

   All common sequence format are supported.

4.0 OUTPUT FILE FORMAT

   The output file contains 7 columns as follows:
     * (1) Sequence number (sequential order in input file) of first
       sequence of a pair.
     * (2) Accesion number of first sequence of a pair.
     * (3) A ':' is always given.
     * (4) Sequence number of second sequence.
     * (5) Accesion number of second sequence.
     * (6) A ':' is always given.
     * (7) Sequence similarity value (2dp).

  Output files for usage example

  File: swtiny1.out

1 Q9WVI4 : 2 Q9ERL9 : 90.48
1 Q9WVI4 : 3 Q9DGG6 : 55.70
1 Q9WVI4 : 4 Q99396 : 54.74
1 Q9WVI4 : 5 Q99280 : 57.66
2 Q9ERL9 : 3 Q9DGG6 : 58.28
2 Q9ERL9 : 4 Q99396 : 56.39
2 Q9ERL9 : 5 Q99280 : 62.31
3 Q9DGG6 : 4 Q99396 : 52.26
3 Q9DGG6 : 5 Q99280 : 53.99
4 Q99396 : 5 Q99280 : 83.41

  File: swtiny2.out

1 O58452 : 2 O30129 : 82.42
1 O58452 : 3 O26938 : 75.56
2 O30129 : 3 O26938 : 71.43

  File: ALLVERSUSALL.log

//
/ebi/services/idata/pmr/hgmp/test/data/structure/allversusall/swtiny1.fasta
//
/ebi/services/idata/pmr/hgmp/test/data/structure/allversusall/swtiny2.fasta

5.0 DATA FILES

   ALLVERSUSALL uses a residue substitution matrix.

6.0 USAGE

  6.1 COMMAND LINE ARGUMENTS

   Standard (Mandatory) qualifiers:
  [-seqinpath]         dirlist    This option specifies the location of
                                  sequence files (input)
  [-datoutdir]         outdir     This option specifies the location of
                                  sequence similarity data files (output).
   -logfile            outfile    This option specifies the name of
                                  ALLVERSUSALL log file (output). The log file
                                  contains messages about any errors arising
                                  while ALLVERSUSALL ran.

   Additional (Optional) qualifiers:
   -matrix             matrixf    This option specifies the residue
                                  substitution matrix that is used for
                                  sequence comparison.
   -gapopen            float      This option specifies the gap insertion
                                  penalty. The gap insertion penalty is the
                                  score taken away when a gap is created. The
                                  best value depends on the choice of
                                  comparison matrix. The default value assumes
                                  you are using the EBLOSUM62 matrix for
                                  protein sequences, and the EDNAFULL matrix
                                  for nucleotide sequences.
   -gapextend          float      This option specifies the gap extension
                                  penalty. The gap extension, penalty is added
                                  to the standard gap penalty for each base
                                  or residue in the gap. This is how long gaps
                                  are penalized. Usually you will expect a
                                  few long gaps rather than many short gaps,
                                  so the gap extension penalty should be lower
                                  than the gap penalty. An exception is where
                                  one or both sequences are single reads with
                                  possible sequencing errors in which case
                                  you would expect many single base gaps. You
                                  can get this result by setting the gap open
                                  penalty to zero (or very low) and using the
                                  gap extension penalty to control gap
                                  scoring.

   Advanced (Unprompted) qualifiers: (none)
   Associated qualifiers:

   "-logfile" associated qualifiers
   -odirectory         string     Output directory

   General qualifiers:
   -auto               boolean    Turn off prompts
   -stdout             boolean    Write standard output
   -filter             boolean    Read standard input, write standard output
   -options            boolean    Prompt for standard and additional values
   -debug              boolean    Write debug output to program.dbg
   -verbose            boolean    Report some/full command line options
   -help               boolean    Report command line options. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose
   -warning            boolean    Report warnings
   -error              boolean    Report errors
   -fatal              boolean    Report fatal errors
   -die                boolean    Report deaths


   Standard (Mandatory) qualifiers Allowed values Default
   [-seqinpath]
   (Parameter 1) This option specifies the location of sequence files
   (input) Directory with files ./
   [-datoutdir]
   (Parameter 2) This option specifies the location of sequence
   similarity data files (output). Output directory ./
   -logfile This option specifies the name of ALLVERSUSALL log file
   (output). The log file contains messages about any errors arising
   while ALLVERSUSALL ran. Output file ALLVERSUSALL.log
   Additional (Optional) qualifiers Allowed values Default
   -matrix This option specifies the residue substitution matrix that is
   used for sequence comparison. Comparison matrix file in EMBOSS data
   path EBLOSUM62
   -gapopen This option specifies the gap insertion penalty. The gap
   insertion penalty is the score taken away when a gap is created. The
   best value depends on the choice of comparison matrix. The default
   value assumes you are using the EBLOSUM62 matrix for protein
   sequences, and the EDNAFULL matrix for nucleotide sequences. Floating
   point number from 1.0 to 100.0 10.0 for any sequence
   -gapextend This option specifies the gap extension penalty. The gap
   extension, penalty is added to the standard gap penalty for each base
   or residue in the gap. This is how long gaps are penalized. Usually
   you will expect a few long gaps rather than many short gaps, so the
   gap extension penalty should be lower than the gap penalty. An
   exception is where one or both sequences are single reads with
   possible sequencing errors in which case you would expect many single
   base gaps. You can get this result by setting the gap open penalty to
   zero (or very low) and using the gap extension penalty to control gap
   scoring. Floating point number from 0.0 to 10.0 0.5 for any sequence
   Advanced (Unprompted) qualifiers Allowed values Default
   (none)

  6.2 EXAMPLE SESSION

   An example of interactive use of ALLVERSUSALL is shown below. Here is
   a sample session with allversusall


% allversusall 
Does an all-versus-all global alignment for each set of sequences in an
input directory and writes files of sequence similarity values
Location of sequence files (input [./]: allversusall/
Location of sequence similarity data files (output) [./]: 
Name allversusall log file (output) [ALLVERSUSALL.log]: 

Processing /ebi/services/idata/pmr/hgmp/test/data/structure/allversusall/swtiny
1.fasta
Processing /ebi/services/idata/pmr/hgmp/test/data/structure/allversusall/swtiny
2.fasta

   Go to the output files for this example

   Files of sequence sets were read from test_data/allversusall/in and
   files of sequence similarity values were written to
   test_data/allversusall/. The log file
   test_data/allversusall/ALLVERSUSALL.log was written. The file path and
   extension of the input and output files was specified in the ACD file.
   The default gap insertion, extension and residue substitution matrix
   were used.

7.0 KNOWN BUGS & WARNINGS

   None.

8.0 NOTES

  8.1 GLOSSARY OF FILE TYPES

   FILE TYPE FORMAT DESCRIPTION CREATED BY SEE ALSO
   Domain hits file DHF format (FASTA-like). 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. SEQSEARCH
   (hits retrieved by PSIBLAST). SIGSCAN (hits retrieved by sparse
   protein signature). LIBSCAN (hits retrieved by various types of HMM
   and profile). N.A.

9.0 DESCRIPTION

   All-versus-all sequence comparisons are commonly required.
   ALLVERSUSALL performs a full global pair-wise alignment for every
   permutation of pair of sequence in each input set of sequences. It
   writes a file of sequence similarity values for each input set of
   sequences.

10.0 ALGORITHM

   Standard N&W type alignment.

11.0 RELATED APPLICATIONS

See also

   Program name Description
   aaindexextract Extract data from AAINDEX
   cathparse Reads raw CATH classification files and writes DCF file
   (domain classification file)
   cutgextract Extract data from CUTG
   domainer Reads CCF files (clean coordinate files) for proteins and
   writes CCF files for domains, taken from a DCF file (domain
   classification file)
   domainnr Removes redundant domains from a DCF file (domain
   classification file). The file must contain domain sequence
   information, which can be added by using DOMAINSEQS
   domainseqs Adds sequence records to a DCF file (domain classification
   file)
   domainsse Adds secondary structure records to a DCF file (domain
   classification file)
   hetparse Converts raw dictionary of heterogen groups to a file in
   EMBL-like format
   pdbparse Parses PDB files and writes CCF files (clean coordinate
   files) for proteins
   pdbplus Add residue solvent accessibility and secondary structure data
   to a CCF file (clean coordinate file) for a protein or domain
   pdbtosp Convert raw swissprot:PDB equivalence file to EMBL-like format
   printsextract Extract data from PRINTS
   prosextract Builds the PROSITE motif database for patmatmotifs to
   search
   rebaseextract Extract data from REBASE
   scopparse Reads raw SCOP classification files and writes a DCF file
   (domain classification file)
   seqnr Removes redundancy from DHF files (domain hits files) or other
   files of sequences
   sites Reads CCF files (clean coordinate files) and writes CON files
   (contact files) of residue-ligand contact data for domains in a DCF
   file (domain classification file)
   ssematch Searches a DCF file (domain classification file) for
   secondary structure matches
   tfextract Extract data from TRANSFAC

12.0 DIAGNOSTIC ERROR MESSAGES

   None.

13.0 AUTHORS

   Jon Ison (jison@rfcgr.mrc.ac.uk)
   MRC Rosalind Franklin Centre for Genomics Research Wellcome Trust
   Genome Campus, Hinxton, Cambridge, CB10 1SB, UK

14.0 REFERENCES

   Please cite the authors and EMBOSS.
   Rice P, Bleasby A.J. 2000. EMBOSS - The European Molecular Biology
   Open Software Suite. Trends in Genetics, 15:276-278. See also
   http://www.uk.embnet.org/Software/EMBOSS

  14.1 Other useful references
