ALIGN0: Compute the global alignment of two protein or DNA sequences without penalizing for end-gaps (Myers and Miller,CABIOS)



your e-mail
( = required, = conditionally required)


First sequence : please enter either :

  1. the name of a file:
  2. or the actual data here:

(sequence format)


Second sequence : please enter either :

  1. the name of a file:
  2. or the actual data here:

(sequence format)


Score options


Report options


Score options

Penalty for opening a a gap (-12 by default for align with proteins, -16 for DNA) (-f)
Penalty for additional residues in a gap(-2 by default for align with proteins, -4 for DNA) (-g)

Scoring matrix file (-s)

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Report options

output line length for sequence alignments (max. 200) (-w)

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your e-mail

Some explanations about the options


Main parameters
enter either the name of a file or the actual data
if you are using Netscape 2.x or later, you can select a file by typing its name, or better, by selecting it with the Netscape file browser (Browse button)
OR you can type your data in the next area, or cut and paste it from another application.
(but not both)

Sequence format
The sequence will be automatically converted in the format needed for the program
providing you enter a sequence either:
in plain (raw) sequence format or in one of the following known formats:
IG,GenBank,NBRF,EMBL,GCG,DNAStrider,Fitch,fasta,Phylip,PIR,MSF,ASN,PAUP,CLUSTALW

References:

Pearson, W. R. (1999) Flexible sequence similarity searching with the FASTA3 program package. Methods in Molecular Biology

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

W. R. Pearson (1998) Empirical statistical estimates for sequence similarity searches. In J. Mol. Biol. 276:71-84

Pearson, W. R. (1996) Effective protein sequence comparison. In Meth. Enz., R. F. Doolittle, ed. (San Diego: Academic Press) 266:227-258

Pise form generator version: 5.a (29 Jun 2005 12:31)