User: bio90029

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bio9002910
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Posts by bio90029

<prev • 39 results • page 1 of 4 • next >
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How to add the misssing bases to a DNA sequence according to the hsp.start, and missing bases
... Hi, I am working on a python script to curate the DNA sequence of a few genes. I initially perform a local blast, and now I am trying to add the missing bases. I have been trying and changing my script but I cannot get the right solution, and I keeping messing up and getting frustrated. I write belo ...
python biopython written 18 days ago by bio9002910
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Comment: C: added missing bases at the beginning of a sequences
... Thanks, but how do I know if the bases are missing at the end or the beginning of the sequences? What part of the blast xml allow me to get that information? Thanks ...
written 27 days ago by bio9002910
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how to get the strand from a blast xml file
... Hi, I am working with a blast xml as the one below: 2 gnl|BL_ORD_ID|79 NODE_82_length_56137_cov_22.281775 79 56195 1 80.5295 46 3.65762e-15 274 515 17046 17290 ...
python biopython written 28 days ago by bio9002910
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added missing bases at the beginning of a sequences
... Hi, I have performed blast on the same gene but from different bacterial strain. Now, I would like to curate the extracted sequences. Some of the genes have missing bases at the beginning of the sequence and others at the end of the sequence. I am trying to work out how I can find out if the missing ...
python biopython written 29 days ago by bio9002910
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Changing a record sequence for another sequence
... Hi, Is there any method that I can use to change the DNA sequence of a record with another sequence? I am just working on a script to curate gene sequence from a fasta file. I have managed to do and extract everything I need to in order to add missing bases. Now my final steps is to replace the sequ ...
python biopython written 7 weeks ago by bio9002910
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Comment: C: problems to split fasta files with biopython scripts
... Hi, Thanks. I found where the problem lied. When, I was preparing a little file to post it for you, I saw something odd. I noticed that I had 96 sequences per gene instead of the 93. So I deleted the bad file, and run the full script (this one has several def():), and I got the right file, and it wa ...
written 10 weeks ago by bio9002910
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Comment: C: problems to split fasta files with biopython scripts
... Hi, Yes, you understood right. I know it doesn't split by name. By the file I tried to split is order, and the first 93 sequences are gene-1, and the following 93 are gene_2, and so on. So I thought that by adjusting the batch size to 93, it would split the file, and produce the files I need it. But ...
written 10 weeks ago by bio9002910
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Comment: C: problems to split fasta files with biopython scripts
... It doesn't give an error as it does the iteration. But instead of producing files with 93 sequences on each, it duplicates the files producing two files with 93 sequences per gene id i.e. gene_1, and then it does produce other files with mixed gene id i.e., gene_1 + gene_1001. The identation is the ...
written 10 weeks ago by bio9002910
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problems to split fasta files with biopython scripts
... Hi, I have a large fasta file about ~200,000 KB. The files consist of around 1800 genes, more or less the structure of the file is : >gene_1 ['chromosomal replication initiator protein'] H15100067005-3045-2-1_gnl|BL_ORD_ID|87 NODE_88_length_41459_cov_22.304518 seq >gene_1 [' ...
python biopython written 10 weeks ago by bio9002910
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Comment: C: Concatenate Multiple .Fasta Files
... Sorry, I got mistaken. ...
written 11 weeks ago by bio9002910

Latest awards to bio90029

Scholar 11 weeks ago, created an answer that has been accepted. For A: from blast xml to fasta file with python
Scholar 12 weeks ago, created an answer that has been accepted. For A: from blast xml to fasta file with python
Scholar 12 weeks ago, created an answer that has been accepted. For A: from blast xml to fasta file with python

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