Question: Pairwise Sequence Alignment Of A Collection Of Proteins Scores In Matrix Format
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gravatar for Azam
9.9 years ago by
Azam50
Azam50 wrote:

I am looking for the pairwise sequence alignments of a collection of proteins, and I want the alignment scores in matrix format. How can I get pairwise alignment score matrix using T-Coffee or other alignment programme?

ADD COMMENTlink modified 9.9 years ago by Spitshine640 • written 9.9 years ago by Azam50

I think you need to provide us with a bit more detail. Do the proteins all belong the same family so that you can make a multiple alignment, based on which you would then extract the similarity/distance between any two proteins.

ADD REPLYlink written 9.9 years ago by Lars Juhl Jensen11k

Proteins belongs to two species of Bacteria

ADD REPLYlink written 9.9 years ago by Azam50
1
gravatar for Spitshine
9.9 years ago by
Spitshine640
Esch-sur-Alzette, Luxembourg
Spitshine640 wrote:

The canonical answer would be to use the phylip package protdist. The EMBOSS package might be easier to use http://emboss.bioinformatics.nl/cgi-bin/emboss/help/fprotdist

ADD COMMENTlink modified 16 months ago by _r_am32k • written 9.9 years ago by Spitshine640

I'd do the same if the sequences are aligned.

The pairwise alignment scores used by alignment programs are usually worse than the ones derived from the alignment.

ADD REPLYlink written 9.9 years ago by Andreas2.5k
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