D I S C

Smith and Waterman Homology Search

MPsrch - PP/PPA

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 :
  1. E-mail address & Query Sequence entry.
  2. Search Control Parameters.
  3. 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) 
   
 Validate address at submission 
 
 Recieve result in: 
   *When you choose "HTML document",you may not be able to get your result well 
   owing to the kind of browser or mail-tool.

 Your Protein Query Sequence:
 

 Your Query Comment:  -  mandatory 
 

 Your name:  -  mandatory

2. Search Control Parameters (return to top)
1) Your Specifying Database :
daily updated PROTEIN ALL(SwissProt+PIR+GenPept+PDB)
PIR SwissProt GenPept PDB PDB_NEW PDB_ALL TRCSM(experimental)
2) Your Defining a Search:
You can choose PP(non affine gap search) or PPA(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 14. Range of acceptable values 0 to 60.
Entering "0" will make the program choose the optimal gap penalty for your PAM table.
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.
5) Your Specifying Matching TABLE :
You can use the following tables. The default is UNSET;
UNSET blosum50 blosum60 blosum70 blosum100 unitprotable
6) Your Specifying PAM Matrix :
You can set the number of Dayhoff PAMs for the comparision score table.
Default( recommended ) is PAM 100. Range of acceptable values 1 to 500. If you want to select UNSET, please input value "0".
If you use PAM parameter, the TABLE parameter is automatically unset.
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.
3) Your Requesting alignment MODE:
The style of alignment are Edinburgh and IntelliGenetics Suite style.
Default is Edinburgh.
4) Your Requesting Ranking Method:
You can choose to rank results by score(SC), or by the Edinburgh Ranking Function(RF).
Default is SC.