Sequence search using a pattern

Question

[amarpreetsabharwal]

How can I retrieve complete amino acid sequences in fasta format from the non-redundant bacterial amino acid fasta file (downloaded and concatenated) using a known string of 8 amino acids that occur in continuity at the end of my sequence of interest?

[Pierre Lindenbaum]

what did you find so far ?

[amarpreetsabharwal]

Pierre,

Thanks for you reply. I am not a bioinformatician or a computer programmer. However, so far, I have found that grep can be used to search for my query but this does not necessarily give me results that are at the end of the sequence and also I do not know how to extract full sequences using grep based on my 8 amino acid query.

Thanks

Amar

Answer 1

[shenwei356]

Similar post: A: String research in a fasta file

Use SeqKit to search sequence pattern in the last 100 amino acid

seqkit grep --by-seq --region -100:-1 --ignore-case --use-regexp --pattern TCTGACC Seq.fa > result.fa

Answer 2

[amarpreetsabharwal]

shenwei356,

Thank you very much for your help.

Amar

Answer 3

[amarpreetsabharwal]

shenwei356, Your suggestion works well but i am getting the following message on terminal after some results:

panic: runtime error: slice bounds out of range

goroutine 1 [running]: panic(0x308920, 0x10838030) /usr/local/app/go/src/runtime/panic.go:500 +0x325 github.com/shenwei356/bio/seq.(Seq).SubSeq(0x10d9dad0, 0x0, 0x7, 0x0) /home/shenwei/shenwei/script/Go/project/src/github.com/shenwei356/bio/seq/Seq.go:121 +0x442 github.com/shenwei356/seqkit/seqkit/cmd.glob..func5(0x4a8c00 0x108da8c0, 0x1, 0x8) /home/shenwei/shenwei/script/Go/project/src/github.com/shenwei356/seqkit/seqkit/cmd/grep.go:195 +0x10e3 github.com/spf13/cobra.(Command).execute(0x4a8c00, 0x108da740, 0x8, 0x8, 0x0, 0x0) /home/shenwei/shenwei/script/Go/project/src/github.com/spf13/cobra/command.go:636 +0x676 github.com/spf13/cobra.(Command).ExecuteC(0x4a92c0, 0x4a8c00, 0x0, 0x0) /home/shenwei/shenwei/script/Go/project/src/github.com/spf13/cobra/command.go:722 +0x397 github.com/spf13/cobra.(Command).Execute(0x4a92c0, 0x0, 0x0) /home/shenwei/shenwei/script/Go/project/src/github.com/spf13/cobra/command.go:681 +0x25 github.com/shenwei356/seqkit/seqkit/cmd.Execute() /home/shenwei/shenwei/script/Go/project/src/github.com/shenwei356/seqkit/seqkit/cmd/root.go:52 +0x21 main.main() /home/shenwei/shenwei/script/Go/project/src/github.com/shenwei356/seqkit/seqkit/main.go:48 +0x11

Let me know what you think of this.

Amar

[shenwei356]

Please click ADD COMMENT to respond to a answer, not create new answers.

it seems a bug. You may have sequences shorter than 100aa, please change or discard the arguments depending on your case

[shenwei356]

I've fixed this bug in v0.3.9, Please download the latest version.