grep DNA after a pattern

Question

[amitpande74]

HI,

I have DNA sequences like these :

and I want to keep all sequences after this pattern "ACTTAAGTGTATGTAAACTTCCGACTTCAACTG" beginning with "TA". I tried

grep -v "ACTTAAGTGTATGTAAACTTCCGACTTCAACTG" file.txt

but it does not work.

Kindly help.

[lakhujanivijay]

Please go through this post to add images properly in the post

A: How to add images to a Biostars post

Also, do you want to get rid of "ACTTAAGTGTATGTAAACTTCCGACTTCAACTG" ?

[Jean-Karim Heriche]

Not sure what you mean. If you want sequences that start with the pattern followed by TA then look for the whole thing, i.e. ACTTAAGTGTATGTAAACTTCCGACTTCAACTGTA

[amitpande74]

@ lakhujanivijay yes

Answer 1

[Benn]

Your code (grep -v) selects only lines that do not have the string ACTTAAGTGTATGTAAACTTCCGACTTCAACTG, so zero. If you want to select only ACTTAAGTGTATGTAAACTTCCGACTTCAACTG followed by AT, but dropping the ACTTAAGTGTATGTAAACTTCCGACTTCAACTG string, you can use grep in combo with sed.

grep "ACTTAAGTGTATGTAAACTTCCGACTTCAACTGTA" file.txt | sed "s/ACTTAAGTGTATGTAAACTTCCGACTTCAACTGTA/TA/g"