Question: Substitution Rate Calculation From Protein Alignment
3
gravatar for Raghul
7.8 years ago by
Raghul200
Italy
Raghul200 wrote:

Hi to all I have blast output for many sequences with only one aligment in the output (blast-options numalignments 1 numdescriptions 1) done with Paramecium protein database. I want to count the substitution for all amino acids with respect to query sequence. ie.How many times Gly replaced by Val in subject, etc. From this output/data I want to calculate log-odds score for protein substitution levels between these 2 species. Are tools available to do this or make such things easier or I have to write (perl-which I know) scripts.

Anybody wants to improve the question for clarity or accuracy feel free to do it!

There is one tool that does something like that but not exactly http://www.ncbi.nlm.nih.gov/pubmed/12854978 MatGAT: an application that generates similarity/identity matrices using protein or DNA sequences.

thank you raghul

alignment scoring • 2.8k views
ADD COMMENTlink modified 7.4 years ago by Alastair Kerr5.2k • written 7.8 years ago by Raghul200
1
gravatar for Alastair Kerr
7.8 years ago by
Alastair Kerr5.2k
The University of Edinburgh, UK
Alastair Kerr5.2k wrote:

I would be concerned using BLAST to generate this information as the same region can be found in multiple HSP/MSP's. Moreover you will lose a lot in information just taking the top HSP. I would use BLAST to gather the sequences you are interested in and use a program such as muscle or probcons to generate the alignment.

The prophecy program from EMBOSS can create a matrix from which that you can calculate this information but would still need some parsing in a scripting language of you choice.

ADD COMMENTlink modified 7.8 years ago • written 7.8 years ago by Alastair Kerr5.2k

I want to calculate the substitution rate between 2 closely related species only. For eg,I have translated protein sequences (partial & full CDS) from transcriptome of Tetrahymena malaccensis.So I want to calculate the substitution rate of amino acids between Tetrahymena malaccensis & Tetrahymena thermophila to notice amino acid changes that could have contributed to the thermophilic lifestyle of T.thermophila. Hope my explanation is ok thank for the reply raghul

ADD REPLYlink written 7.8 years ago by Raghul200

Above still applies: just use blast to get the orthologs.

ADD REPLYlink written 7.8 years ago by Alastair Kerr5.2k

ok thanks. Can you reference a publication that explains clearly (to an extent), so I can learn better.

ADD REPLYlink written 7.8 years ago by Raghul200
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