User: bio90029

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bio9002910
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Posts by bio90029

<prev • 44 results • page 1 of 5 • next >
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Comment: C: how to get the strand from a blast xml file
... Thanks, Unluckily, I cannot used grep as I wanted it as part of a python programme I was working on. By now I had finished it. I worked out the strand by the start and end positions. ...
written 24 days ago by bio9002910
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Comment: C: allelic phylogenic clustrering or tree
... ramesh.8v,; That looks good, thanks. ...
written 24 days ago by bio9002910
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allelic phylogenic clustrering or tree
... HI, I have carried a wgMLST profile from various bacterial strain, and I am interesting in drawing a allelic phylogeinc tree. I have seen that R can produce phylogenic trees but I am having loads of problems trying to find a decent tutorial. I know that R uses the "ape" package but I don't find whi ...
R biopython python written 5 weeks ago by bio9002910
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Comment: C: bacterial virulent genes
... Hi, that is a nice database but unluckily it does not hold any information about Enterobacter. I sent them a feedback suggesting the addition of the species. ...
written 8 weeks ago by bio9002910
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bacterial virulent genes
... Hi, I was wondering if someone can help me with the following. I am interested in producing a python dictionary with gene name and sequence for *Enterobacter spp*. I have been trying to do a search in NCBI, I can get plasmids encoding for antibiotic resistance but not virulence genes that damage th ...
gene genome written 8 weeks ago by bio9002910
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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 11 weeks 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 3 months 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 3 months ago by bio9002910 • updated 29 days ago by toralmanvar90
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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 3 months 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 3 months ago by bio9002910

Latest awards to bio90029

Scholar 4 months ago, created an answer that has been accepted. For A: from blast xml to fasta file with python
Scholar 4 months ago, created an answer that has been accepted. For A: from blast xml to fasta file with python
Scholar 4 months ago, created an answer that has been accepted. For A: from blast xml to fasta file with python

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