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Cool would do that thanks!

I am sorry If I offended someone in any way! I am really new to this forum and yes I am learning the rules now. I never meant to hijack any threads!! It's just that I was in a difficult situation and...

I have a file1 as
>NC_0123
>NC_0124
>NC_0125

and file 2
>NC_0123
ACGTGCGTC
>NC_0125
ACTGCGTCGTCG
>NC_0126
ACTGCGTGCGTCG

i want the output as
>NC_0123
ACGTGCGTC
>NC_0125...

u can try cat MasterFile.txt | grep -f - Pattern.txt

this should work

Bravo!! Thanks a ton again!! :D

Thanks guys for the code n yeah for correcting my interpretation of sed! somehow the third answer seems to be working with my requirements..havnt really used awk in my work earlier..so explanations...

I have a similar doubt
i have my input file as follows:
>some lines of text
actgtg
aaactgtg
acgtcg
>some lines of text
acgtgc
agtcgt
ttgcgt
etc..etc

i want the output as
>some lines of...