Homology Search by Smith and Waterman Method

Smith and Waterman Homology Search

MPsrch -NN/NNA

MPsrch is a trademark of the University of Edinburgh. Its runs on our MasPar massive parallel computer system, consisting of a DECStation. MPsrch Reference Manual contains reference infomation and instruction for using MPsrch.
This page is to submit your e-mail homology search by using the MPsrch based on Smith and Waterman full dynamic algorithm. You can get your search result at your e-mail address!

Step to fill out in this form :

E-mail address & Query Sequence entry.
Search Control Parameters.
Output Parameters.

Please click here if you can get quick help of our MPsrch e-mail service.
support@dna.affrc.go.jp

return to DISC Home Page or Homology Search on DISC or DISC MPsrch.

1. E-mail address & Query Sequence (return to top)


 Important! Please fill out  your e-mail address: 
 (receiving your search result) 
 
 
 Your Nucleotide Query Sequence:
 

 Your Query Comment:  -  mandatory 
 

 Your name:  -  mandatory

2. Search Control Parameters (return to top)

1) Your Specifying Database :

daily updated DNA ALL(DDBJ+GenBank+EMBL)

MAFF DNA

JAPIO

bct est hum inv man org pat phg pln pri rna rod sts syn una vrl vrt

bct est inv man pat phg pln pri rna rod sts syn una vrl vrt

est inv man org pat phg pln pri rna rod sts syn una vrl vrt

bct est inv man org pat phg pln pri rna rod sts syn una vrl vrt

GB-CDS is a CDS database extracted from GenBank Rel.90(Aug.95) 
by NAKAMURA Yasukazu (yanakamu@lab.nig.ac.jp)

  DDBJ, GENBANK, EMBL and GB-CDS databases are able to 
  select those division. Choose division option, 
  if you want to select division databases.

2) Your Defining a Search:
You can choose NN(non affine gap search) or NNA(affine gap search).

3) Your Specifying Gap Penalty(non affine gap search only):
GAP penalty, in the Smith-Waterman algorithm, is applied to any unmatched base or residue in the alignment.
Default is 6. Range of acceptable values 2 to 60.

4) Your Specifying Gap Penalty(affine gap search only):
GAPOPEN sets to start a gap in the alignment.
Default is 20. Range of acceptable values 2 to 60.
GAPEXTEND applied to extend an alignment beyond an existing gap. Default is 6. Range of acceptable values 2 to 60.
GAPEXTEND must always be less than or equal to GAPOPEN.

You can use the following tables ;
Default jmetric

3. Output Parameters (return to top)

1) Your Requesting SUMMARY List :
Summary is the number of one-line sumamries of names and scores in your output.
SUMMARY:
Default is 20. Maximum is 200.

2) Your Requesting ALIGNment:
Alignment is the number of alignments to be displayed in your output.
ALIGN:
Default is 20. Maximum is 200.

Default is Edinburgh.