User: david

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david0
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Posts by david

<prev • 9 results • page 1 of 1 • next >
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Ignore Error "Multiple Sequences Found With Same Name" In Clustalw
... Hi, I have a python program generating a clustalw2 alignment of about 500 sequences from a fasta file. The names of the sequences correspond to the respective organisms plus the substrate specificity of a given sequence. Therefore quite a few of these names are identical and i get the error message ...
clustalw biopython written 4.9 years ago by david0 • updated 10 weeks ago by Biostar ♦♦ 20
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Comment: C: How To Sort A Ncbiwww.Qblast Output By Score?
... Thanks a lot Peter! The magic completely solved it :). maybe you can help me with an even easier problem. I now get the best hit ID as a string looking like this: gi|3318718|pdb|1AMU|A. I want to use it to fetch the corresponding sequence with Entrez.efetch. In order to do this I would need to get t ...
written 5.0 years ago by david0
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Comment: C: How To Sort A Ncbiwww.Qblast Output By Score?
... the blast output is a xml file. i then use the ncbixml parser. i need the id of the best hit. however, this best hit is always according to e value, not to score result_handle = NCBIWWW.qblast("blastp","nr", query_str) blast_records = NCBIXML.parse(result_handle) for record in blast_records: i ...
written 5.0 years ago by david0
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How To Sort A Ncbiwww.Qblast Output By Score?
... I try to write a Biopython script that performs a blast search and returns the id of the first hit. Although my python skills are rather rudimentary, this seems to work. But for my specific purpose it would be better if the script returns the first hit according to Blast score, not E value. Is it po ...
biopython written 5.0 years ago by david0 • updated 5.0 years ago by Peter5.6k
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Comment: C: Expanding Multiple Sequences In Fasta File
... hi saggisardar, I have a list of 100 amino acid stretches. I need to find the original sequence for each query, identify the domain that contains the 100 amino acid stretches in this original sequence and replace all stretches in the initial list with the thus found domain sequence. I'm now writing ...
written 5.0 years ago by david0
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Comment: C: Expanding Multiple Sequences In Fasta File
... Sorry for the confusion. What i need is a dataset of the full sequences of homologous domains (as many as possible) from a given protein class. There is a publication where they use a library of amino acid stretches (from homologous proteins) as a training set for their algorithm. However these stre ...
written 5.0 years ago by david0
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Comment: C: Expanding Multiple Sequences In Fasta File
... because the proteins are NRPS, so they have a lot of domains and i only need the one that partly aligns with my stretches. ...
written 5.0 years ago by david0
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Expanding Multiple Sequences In Fasta File
... I have a fasta file with sequences of about 100 amino acids and i need to expand them on both sides with the corresponding amino acids to get a fasta file that contains the entire domain sequences instead of the 100 amino acid stretches. I try to write a biophyton script that does the job, but i'm a ...
blast written 5.0 years ago by david0 • updated 5.0 years ago by SaggiSardar20
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Comment: C: Converting Taxonomic Lineages Into A Common Tree
... hey pierre. thanks a lot for this solution. probably a stupid question but i'm a biochemist and this is my first java program ever. i've compiled your program on my mac os x 10.8 and want to run it now, but it just goes into an endless loop. how is the input (the list) specified. thx! ...
written 5.0 years ago by david0

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