User: Jason

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Jason0
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Posts by Jason

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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 19 days ago by Jason0 • updated 19 days ago by benformatics270
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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 4 months ago by Jason0 • updated 4 months ago by cpad01128.8k
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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 5 months ago by Jason0
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Comment: C: find difference sequences with different header
... Hi, This code will do same mistake because some sequences in file 2 have different id but same identical sequences in file 1. We get all sequences from file1 that do not match the IDs in common_ids and store the result in file3.fa, but the problem here some sequences in file 2 have different index ...
written 5 months ago by Jason0
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Comment: C: find difference sequences with different header
... Hello, After I made some analysis for many sequences I found this code will hold some common sequences in both file 1 and file 2 and save that in file 3 Find common sequences between file1 and file2 and extract ther IDs: seqkit common -s file1.fa file2.fa|grep '>'|cut -c2- > common_ids Ge ...
written 5 months ago by Jason0
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Comment: C: find difference sequences with different header
... Hey, This code did not do what I expect it. thanks ...
written 5 months ago by Jason0
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Comment: C: find difference sequences with different header
... Thank you so much for your hep ...
written 5 months ago by Jason0
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Comment: C: find difference sequences with different header
... Hey, I applied this code cat file1.fasta file2.fasta|seqkit rmdup -s -o file3.fa the result saved in file3 as : >NP_000009.1 very long-chain specific acyl-CoA dehydrogenase, mitochondrial isoform 1 precursor [Homo sapiens] MQAARMAASLGRQLLRLGGGSSRLTALLGQPRPGPARRPYAGGAAQLALDKSDSHPSDALTRK ...
written 5 months ago by Jason0 • updated 5 months ago by genomax55k
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Comment: C: find difference sequences with different header
... Hey, When I used this command it gave me this error and i'm sure about the name of files: cat file1.fasta file2.fasta|seqkit rmdup seqkit rmdup -s -o file3.fa [ERRO] fastx: open seqkit: no such file or directory How can I resolve this problem? If I change the command to this command cat file1.f ...
written 5 months ago by Jason0
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find difference sequences with different header
... I have two fasta file with 200 sequences. I want to use shell commands to find difference sequences with different headers between theses two fasta files and save that in new file with heder from file as output. this command find match sequences even if header is not same. it look at match sequenc ...
sequence written 5 months ago by Jason0 • updated 5 months ago by cpad01128.8k

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