Searching for homologous sequences of small peptides in several species

BLASTP – Searching for homologous sequences of small peptides in several species

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Hello!

I now have some protein sequences of a number of species (chicken, human, mouse, …). I want to use BLASTP to find the homologous sequence of a small peptide “KPWLRVALCPG” in these species. For the convenience of searching directly for multiple species, I have combined the protein sequences of these species into a single file called “merge.fa” and created a blast database.

I try to filter out peptides with a bit-score > 20 and I use a formula (E = query_sequence_length * total_database_length / 2^bit-score) to calculate the corresponding e_value for a bit-score of 20.

I first searched for merge.fa, using the following command.

blastp -db merge.fa -query test.fa -out test.merge.0 -task blastp-short -outfmt 0 -evalue 5283 -word_size 2 -matrix PAM30

Another search was carried out on chicken.fa, using the following command.

blastp -db chicken.fa -query test.fa -out test.chicken.0 -task blastp-short -outfmt 0 -evalue 44 -word_size 2 -matrix PAM30

However, I found two problems.

  • Firstly, the bit-score threshold was not the expected “20”, but “18”.
  • Secondly, I compared the search results for “chicken.fa” with those for “merge.fa” and found that many of the results for “chicken.fa” had disappeared!

I am very confused, can anyone give me some advice? Thanks.


small


peptide


blastp

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