I have a set of about 1000 homologous protein sequences with high diversity across various genera and families. What I need is to perform BLAST alignment of each possible sequence pair and obtain respective E-scores. Is there a possibility to run only alignment of the pair of sequences from a command line using local instance of BLAST, or a standalone tool implementing the same algorithm?
I specifically need BLAST alignment because my particular interest is focused on its E-scores.
For using BLAST tool, you need a custom database in your case. You can build your custom database from your sequences using this tutorial:
https://www.ncbi.nlm.nih.gov/books/NBK279688/
Then you can run BLAST using your query sequences against custom database using stand alone tool:
https://www.ncbi.nlm.nih.gov/guide/howto/run-blast-local/
Alternatively, you can use MEGA X or BioEdit tools for multiple alignments but I am not sure whether these give E-scores or not.
Hi
The query is a little bit confusing. You want to compare the sequences in pairwise manner and estimate similarity scores or E-values. In Blast program (offline and online) the E-values takes into account the database used .So you need to first ascertain this aspect before going ahead. The local Blast can be performed but you need to create a database and again the E-values will take into account the database used for similarity analysis. If you want to generate and analyze pair-wise scores of comparison, it is stored as temporary files in many programs and can be retrieved for analysis.
Ajay Saini ,
thanks, you are right, I have made quite a silly mistake confusing E-value with sequence similarity. What I wanted is to use pairwise sequence similarities to cluster proteins prior to MSA. Anyway, I have found out that the edit distances (Levenshtein's) also suit my task well.
Hi
Thanks for clarification. however if you still need to generate and analyze pair-wise scores of comparison, it is stored as temporary files prior to generating similarity/distance matrix in some programs and can be retrieved for analysis.
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