kssearch

Function

compares query sequences to databases using SSEARCH

Description

kssearch compares query sequences with databases utilizing SSEARCH (Smith-Waterman Search). SSEARCH does a rigorous Smith-Waterman search for similarity between a query sequence and a group of sequences of the same type (nucleid acid or protein). kssearch utilizes SSEARCH method included in FASTA SOAP service provided by EBI (European Bioinformatics Institute).Original web-service is located at the following URL:

http://www.ebi.ac.uk/Tools/webservices/services/sss/fasta_rest

This tools is a subset of Keio Bioinformatics Web Service (KBWS) package, which contains interfaces to bioinformatics web services through a proxy server at Keio University. kssearch is an interface of "runSSearch" method included in KBWS SOAP service.
This method can be alternatively accessed directly from programming languages as SOAP web service. Please refer to the KBWS online documentations http://www.g-language.org/kbws/ for more information.

Usage


   Here is a sample session with kssearch

% kssearch
compares query sequences to databases using SSEARCH
Input (gapped) sequence(s): test.fasta
output sequence(s) [nc_000908.kssearch]:

   ### output sample

	  

Command line arguments

Qualifier Type Description Allowed values Default
Standard (Mandatory) qualifiers
[-seqall]
(Parameter 1)
seqall (Gapped) sequence(s) filename and optional format, or reference (input USA) Readable sequence(s) Required
[-database]
(Parameter 2)
string Target database for search Any string Required
[-outfile]
(Parameter 3)
outfile Output file name Output file <*>.kssearch
Additional (Optional) qualifiers
-moltype string molecular type Any string  
-histogram boolean Display histogram Boolean value Yes/No No
-nucleotide boolean your query is nucleotide or not(protein) Boolean value Yes/No No
-topstrand boolean Nucleotide sequence strand to use for seqrch (top) Boolean value Yes/No No
-bottomstrand boolean Nucleotide sequence strand to use for seqrch (bottom) Boolean value Yes/No No
-gapopen integer Score for the initiation of a gap Any integer value 0
-gapext integer Score for each base/residue in a gap Any integer value 0
-scores integer Maximum number of scores displayed in the output Any integer value 0
-alignments integer Maximum number of alignments displayed in the output Any integer value 0
-ktup integer Word size to use for sequence comparisons Any integer value 0
-matrix string Scoring matrix to be used in the search Any string  
-eupper float Upper E-value threshold Any numeric value 0.000
-elower float Lower E-value threshold Any numeric value 0.000
-dbrange string Range of sequence lengths in search database to include in search Any string  
-seqrange string Region of the query sequence to use for the search Any string  
Advanced (Unprompted) qualifiers
(none)

Input file format

kssearch can use any genome sequence data that seqret can read.

Output file format

The output from kssearch is general SSEARCH output file.

Data files

None.

Notes

None.

References

      Pearson, W.R., and Lipman, D.J.,(1988) Improved Tools for Biological
      Sequence Comparison, PNAS, 85, 2444-2448.

      Pearson, W.R.,(1990), Rapid and Sensitive Sequence Comparison with FASTP
      and FASTA, Method in Enzymology, 183, 63-98.

      Mackey, A.J., et al.,(2002) Getting more from less: algorithms for rapid
      protein identification with multiple short peptide sequence. Molecular
      and Cellular Proteomics, 1(2), 139-147.
    

Warnings

None.

Diagnostic Error Messages

None.

Exit status

It always exits with a status of 0.

Known bugs

None.

See also

Program name Description
kblast Search similar sequences in public repositories using BLAST
seqret Reads and writes (returns) sequences

Author(s)

Kazuki Oshita (cory @ g-language.org)
Institute for Advanced Biosciences, Keio University
252-8520 Japan

History

    2009 - Written by Kazuki Oshita
    Mar 2013 - Update document by Kazuki Oshita
               Change option name(d => database) by Kazuki Oshita
    

Target users

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

Comments

None.

Appendix

Ths list for databases about kssearch is available at following URL:
http://soap.g-language.org/kbws/data/db_ssearch