psiblast to get pssm. How to get a pssm from a multiple alignment ?

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5.5 years ago

lagartija ▴ 160

Hi,

I have problems using psiblast this being my command line : psiblast -subject test.fa -in_msa aligment_test.fa -out_ascii_pssm pssm_test1.txt -ignore_msa_master

I get this error message whenever I have more that 4 sequences : BLAST options error: Repeated Seq-IDs detected in multiple sequence alignment file, please ensure all Seq-IDs are unique before proceeding. I am 100% sure I have no repeats and try also adding false sequences to my alignment to check that it would always crash when I have more that 4 sequences.

Do you have any idea of how I could proceed to get PSSMs from multiple alignments ?

Thank you very much in advance for your help, have a nice day

pssm • 2.0k views

ADD COMMENT • link updated 5.5 years ago by Biostar 20 • written 5.5 years ago by lagartija ▴ 160

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Please post an example of your input data.

ADD REPLY • link 5.5 years ago by Joe 21k

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Just headers needed. So grep "^>" test.fa | head -5 would do.

ADD REPLY • link 5.5 years ago by GenoMax 146k

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