User: Jason

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Jason0
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Posts by Jason

<prev • 25 results • page 1 of 3 • next >
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removed entrie sequence include specific letters
... Hey All I need help with shell command or Perl script. I have 400 sequences and some of these sequences have X,B and Z. I want to remove an entire sequence from fasta file that has X, B,Z I found this shell command that will remove only this letter from the sequence sed '/^[^>]/s/[X||Z|B ...
sequencing written 18 days ago by Jason0 • updated 18 days ago by shenwei3564.4k
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Comment: C: grep only specific motif from whole protein sequence
... Hey, Thanks for help but I'm getting error. How can I resolve it awk: syntax error at source line 1 context is >>> {N=match($2,/(S....[FS]...L)/, <<< awk: illegal statement at source line 1 awk: illegal statement at source line 1 ...
written 3 months ago by Jason0 • updated 3 months ago by RamRS20k
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(Closed) grep only specific motif from whole protein sequence
... Hello All, How to Grep only specific motif from complete sequences in a fasta file using shell command? Also, I want to include the lines beginning with a > before these target sequences. I got help from the previous post in this link: https://www.biostars.org/p/339314/#339423 to grep whole sequ ...
sequencing written 3 months ago by Jason0 • updated 3 months ago by Pierre Lindenbaum116k
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Comment: C: grep whole sequences containing a specific motif in a fasta file
... It is working thank u ...
written 4 months ago by Jason0
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Comment: A: grep whole sequences containing a specific motif in a fasta file
... What about if I want to keep only sequences that don’t have the motif” SXXXX (F/S)XXXL” and save that in new fasta file: The result in that case should be only this sequence: sp|Q9re7.2|CARer_HUMAN RecName BKLSVLEGWRVTLTSVIDRFRITPYLRQTKVLNPDDEEQVLSDPNLVIRKRKVGVLLDILQRTGHKGYVAFLESLELYYPQLYKKVTGKEP ...
written 4 months ago by Jason0
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Comment: C: grep whole sequences containing a specific motif in a fasta file
... It was working. thank u so much ...
written 4 months ago by Jason0
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6 follow
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grep whole sequences containing a specific motif in a fasta file
... How to Grep the complete sequences containing a specific motif in a fasta file using shell command? Also, I want to include the lines beginning with a `>` before these target sequences. I found this post :https://www.biostars.org/p/274859/ similar to my problem but I'm looking for different mot ...
sequencing written 4 months ago by Jason0 • updated 3 months ago by Malcolm.Cook940
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5 follow
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Add string to list of protein sequences in fasta file with different lengh
... How can I do this using python or shell command: Suppose I have 200 protein sequences in fasta file named 'proto.fasta' with different lengths I want to find maximum length between these sequences and then I want to add one string (Z) to all other sequences at the end of them to make all sequences ...
sequencing written 4 months ago by Jason0 • updated 4 months ago by benformatics400
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reduce size of string
... Hello all I have txt file of 400 sequences. abcdtmrtnunzaeq ygbwwqwtsazpklf yuncspytaqwercl How can I write shell command to delete the first three letter and also delete the end of the three letter at each row and save that in new txt file Result should be save in new txt file like this: ...
python sequence shell written 8 months ago by Jason0 • updated 8 months ago by cpad011210k
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Comment: C: find difference sequences with different header
... Hi, I also tested your code. It gave me some sequences find in both file 1 and file 2. it will not save sequences in file1 that not find in file 2. The problem here some sequences in file 2 have different index but same identical sequences. That mean some sequences from file 2 will be in result. I ...
written 9 months ago by Jason0

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