User: bioslayer

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bioslayer50
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New User
Location:
New Zealand
Last seen:
4 years, 1 month ago
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5 years, 3 months ago
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Posts by bioslayer

<prev • 9 results • page 1 of 1 • next >
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Comment: C: How to get bacterial gene names if I know their coordinates
... This simplifies it very nicely, I can smoothly make a wrapper for these end points. Going with the E.coli example, suppose I have two entries as follows: 574737    575753    -    4056471    4056555 + So using the first endpoint I will construct a query like this, feature can be anything "CDS, ncR ...
written 4.7 years ago by bioslayer50
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Comment: C: How to get bacterial gene names if I know their coordinates
... Yes, REST was among the options I considered. I saw the Perl client it has and ran through its documentation but I can not really tell how to pass it a genome ID and coordinates for me to get back the gene names. It will be great if you can provide an example of a query to illustrate this. Thanks ...
written 4.7 years ago by bioslayer50
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How to get bacterial gene names if I know their coordinates
... My ultimate goal is to do a comparative GO enrichment analysis on a collection of bacterial genes from over 3000 genomes. Within each genome I have a list of around 100 or so interesting genes, their start/stop coordinate. I have the names and PRODUCT annotation for some of the genes but my parsing ...
gene names coordinates go enrichment written 4.7 years ago by bioslayer50 • updated 4.6 years ago by Biostar ♦♦ 20
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Answer: A: what is the best way to cut a lot of embl file at given position in a way to obt
... The sfetch utility from biosquid can allow you to do that and specify the format you want to extract your sequences in, simply,   sfetch -d file.embl -f 19944 -t 27500 -F fasta .   Note the "."  at the end. You can as well rename the seq you've extracted sfetch -d CP001581.1.embl -f 3 -t 20 ...
written 4.9 years ago by bioslayer50
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Answer: A: smallRNA prediction and InterGenic Regions(IGRs) finding
... I am aware of FeatureExtract http://www.cbs.dtu.dk/services/FeatureExtract/ and RSAT http://rsat.ulb.ac.be/. These two frameworks parse an annotated genome file and allow you to select/filter unannotated regions. Therefore they rely on proper annotation as a prerequisite. If your bacterium is E.coli ...
written 4.9 years ago by bioslayer50
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Comment: C: How to perform phylogeny analyses
... Your answer is very well worded and give a round explanation of phylgenetics. I want to take a chance and ask about some tips. If I have a good quality alignment and want to estimate which sequences is more ancestral to the other one, which algorithm is more appropriate to answering that question ? ...
written 4.9 years ago by bioslayer50
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Answer: A: Finding an exactly conserved amino acid sequence in a particular protein.
... The highest scoring sequences in Blast should give you an insight about the degree of conservation for this region. Try querying your sequence against Pfam http://pfam.xfam.org/ to see if that domain is actually conserved. Another thing you can do is to see which amino acid residues remain conserved ...
written 5.1 years ago by bioslayer50
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Comment: C: 5'UTR in bacterial genomes
... It sure is a mess. An interesting type of mess. Thanks for the clarifications regarding that possibility that convergent and divergent genes could be sharing either the same terminator or promotor. That was insightful In the UTR table, I noticed some genes, like CsrA have several 5` UTRs. That all ...
written 5.1 years ago by bioslayer50
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5'UTR in bacterial genomes
... The gene coordinates table for E.coli looks like the following :   orientation start end gene name +    189    255    thrL +    336     2799    thrA +    2800    3733    thrB +    3733    5020    ...
prokaryotes intergenic regions 5'utr written 5.1 years ago by bioslayer50 • updated 5.1 years ago by Asaf6.1k

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