Regarding fasta file format

Question

[seta]

Hi all,

I have a basic question, I recently got an excel file with two columns, one is gene id and another is protein sequence. I want to make a blast database from these sequences. After copy/pasting those in the Notepad (I know copy/pasting is a wrong task), they are like here:

>839263    MASGGKAKYIIGALIGSFGISYIFDKVISDNKIFGGTTPGTVSNK
>837071    MASLLDKAKDFVADKLTAIPKPEGSVTDVDLKDVNRDSVEYLAKV

Could you please help me out how I can change the excel file to a text file with the correct fasta format?

Thanks

[Matt Shirley]

"Notpad": I like this better than the original name. "Not" useful for much.

Answer 1

[Devon Ryan]

sed -e 's/ \+/\n/' input.txt > output.fa

[seta]

Thanks for your response. But the format was not changed, and the error of "BLAST options error: file.fa does not match input format type, default input type is FASTA" still appears when I try to make blast database.

[Devon Ryan]

Presumably you have a tab between the columns rather than a space, so change the space in the command to \t.

[seta]

yes, it's tab, I try it. thanks