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Stand Alone Blast


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#1 Sukeerthi Teja

Sukeerthi Teja

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Posted 03 May 2011 - 04:16 AM

I basically have these 2 files, the

Input file = sequences.txt
Database file = homologene_result.txt

Isn't "blastall" an older version command ? That is why i was using makeblastdb

This is what i typed

172-30-8-231:bin sukeerthiteja$ makeblastdb -in homologene_result.txt -dbtype prot -parse_seqids -out teja1 blastp -query sequences.txt -db teja2

AND i also tried the code using .txt next to teja2.txt, but in both cases i got this error.

Error: (106.18)
NCBI C++ Exception:
Error: (CArgException::eSynopsis) Too many positional arguments (1), the offending value: blastp
Error: (CArgException::eSynopsis) Application's initialization failed

Please help me understand where exactly i am going wrong.

Thanking you
Teja

#2 HomeBrew

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Posted 03 May 2011 - 12:16 PM

First, you must turn your FASTA formatted sequences into a BLAST database:

formatdb -i input_sequences.fasta -p T -n input_sequences_database_name.db


Then you can BLAST your query sequence(s) against the database you made:

blastall -p blastp -d input_sequences_database_name.db -F F -i query_sequence.fasta -o blast_output_file.txt




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