User: Pablacious
Pablacious • 610
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Posts by Pablacious
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... Hi David, did you get anywhere on this? I'm trying to find the probe sequences for that array unsuccessfully, would you have any clues I could use? Thanks! ...
written 9 months ago by
Pablacious • 610
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... Why would you want to search for a random instance of the motif instead of the whole motif? Using the motif to search is more sensitive than an instance.
...
written 5.4 years ago by
Pablacious • 610
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... The > line in a fasta file is only divided in the identifier part and the description part. The identifier part goes between the > and the first space. Whatever goes after the first space is the description part (which can have all the spaces that you want), so there is no such a thing as a la ...
written 5.4 years ago by
Pablacious • 610
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Answer:
A: Go Enrichment From Protein Id
... For E. coli I would use EcoCyc from SRI. It is probably one of the most comprehensive and curated resources when it comes to E. coli. It has a module for doing enrichment analysis through its smart tables, see here http://ecocyc.org/PToolsWebsiteHowto.shtml#node_toc_node_sec_7.5.1
It might be more ...
written 5.4 years ago by
Pablacious • 610
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... I would use the NCBI Taxonomy, where you can select a particular taxonomic domain and then switch on the counts of available genomes, publications, etc.
Go to http://www.ncbi.nlm.nih.gov/taxonomy/?term=insects
click on Hexapoda and then on the grey rectangle full of check boxes choose what you wa ...
written 5.4 years ago by
Pablacious • 610
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... Dear community,
I'm interested in fetching transcription factor binding sites (the actual locations in the genome) for the upstreams of certain genes in Drosophila melanogaster (fruit fly). ENSEMBL doesn't have a gene regulatory build for fly, as it does for human or mouse. Is anyone aware of a res ...
written 5.4 years ago by
Pablacious • 610
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... Regarding point 2, you probably want to use protein alignments instead of gene based alignments, unless that your species are very close in phylogenetic terms. Regarding point 3, I would recommend you to use the strategy used at ENSEMBL to build your gene trees:
http://www.ensembl.org/info/genome/c ...
written 5.7 years ago by
Pablacious • 610
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... Currently there doesn't seem to be a way of parsing genbank files with biojava3. The only mention of genbank in the whole project seems to be in the DataSource class and some tests that use it (looking at the git project). There is nothing that seems related in the API either. There is a thread in o ...
written 6.3 years ago by
Pablacious • 610
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Comment:
C: Beginner Blasting Short Sequences
... You could also use "water" from the EMBOSS package (another Smith-Waterman algorithm implementation). Totally agree on avoiding the heuristics for data sets of this size. ...
written 7.3 years ago by
Pablacious • 610
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... Thanks Andrew, this looks promising. ...
written 7.6 years ago by
Pablacious • 610
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