User: gaiboyan23

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gaiboyan230
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Posts by gaiboyan23

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Comment: A: Get ASCII-format PSSM from web PSIBLAST
... Hi, I'm not sure if you've solved your problem, but I've a similar question. How did you find a way to convert ASN.1 to ASCII ...
written 14 months ago by gaiboyan230
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PSSM (Position Specific Scoring Matrix) from NCBI convert to matrix format
... When I run psi-blast (3 iterations) to download the PSSM (Position Specific Scoring Matrix), the files come up as ASN.1 files. How can i convert these ASN.1 files to matrices. The PSSMs should look like matrices with 20 columns (for 20 amino acids) and L rows (L=length of protein) However, the file ...
alignment sequence written 14 months ago by gaiboyan230
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Comment: C: too many characters in strings containing long protein sequence ?
... Ah interesting to see someone else working with titin, and thank you for the response. I tried your code and my protein sequence still gets truncated. Is there a way to get the non-truncated sequence (i'm putting them in an excel file)? My proteins are not nearly as long as titin (1000 some residue ...
written 16 months ago by gaiboyan230
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too many characters in strings containing long protein sequence ?
... Using Biopython, I parsed a FASTA file for a list of protein sequences. Everything works, except when the sequence is too long (some are over 1000 characters). A majority of the sequence gets replaced by ..., How can I obtain the entire sequence in my output? Currently my output look like this (I p ...
fasta protein biopython sequencing written 16 months ago by gaiboyan230 • updated 16 months ago by Joe16k
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Comment: C: How to retrieve protein sequences from FASTA by using accession number?
... Yes, i've checked and the accessions match. Here's a the first line of the list of my accession numbers (cut short for space): ['SYAC_HUMAN', 'PGAM4_HUMAN', 'SYEP_HUMAN', 'H14_HUMAN', 'K1C9_HUMAN', 'COPA_HUMAN', 'SYQ_HUMAN', ] Here's from the FASTA file (I only included SYAC_HUMAN, the first ...
written 17 months ago by gaiboyan230 • updated 17 months ago by RamRS27k
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Comment: C: How to retrieve protein sequences from FASTA by using accession number?
... there is no error/ list was generated. I've looked some other posts but they seem to not exactly fit my question/ use different modules/programming language. I'll keep looking I guess ...
written 17 months ago by gaiboyan230
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Comment: C: How to retrieve protein sequences from FASTA by using accession number?
... Just reformmated, first time poster here, thanks for the tip! ...
written 17 months ago by gaiboyan230
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How to retrieve protein sequences from FASTA by using accession number?
... Noobie to bioinformatics here, I'm strugging with a code that shouldn't be hard. I have a list of 800+ accession numbers for proteins of interest, and I'm trying to get the corresponding protein sequence for all of them. I've downloaded the FASTA file from Uniprot, and I'm trying to figure out a w ...
fasta sequence protein written 17 months ago by gaiboyan230 • updated 17 months ago by Joe16k

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