I want to find the protein sequences of wheat which have IGT motif. I used the scanprosite tool to find the protein sequences which have igt motif. 9419 sequences are collected by scanprosite I have 3 other wheat protein sequences, and I want to align 3 protein sequence with 1890 protein sequences by pairwise alignment to check the homology with 3 sequences.what is the best tool for pairwise alignment which can be used to sequence this huge data? By using the tool scanprosit i collected sequences that have the desired motif. now want to check the similarity or homology of these sequences with 3 other protein sequences. Kindly tell me to check the homology what can i do?
1 answer
Give a try to Clustal Omega It is a global alignment program that uses a Hidden Markov Mode.
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Use standalone blast where you can make 1890 protein as a database (using makeblastdb) and rest 3 protein as a query.
This is good advice for local alignment, but if you're looking to do global/MSA, you'd need a different approach. By pairwise alignment, do you mean you wish to align each of the 3 sequences with each of the 1890 other sequences? Because a pairwise alignment means something different in the multiple sequence alignment context.
yes, I want to align 3 protein sequences with 9419.
Where did that come from?
Actually, i want to find the protein sequences of wheat which have IGT motif. I used the scanprosite tool to find the protein sequences which have igt motif. these sequences are collected by scanprosite
Please edit your question and add this information. From the looks of it, you have an XY problem.
check question now please
How long are the sequences?
sorry I mention the wrong number of protein sequences.it is 9419 protein sequences and length vary from 250 to 1500.some protein sequences are uncharacterized.
Would it not be better to do this search against wheat proteome?