User: parism9

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parism930
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Posts by parism9

<prev • 5 results • page 1 of 1 • next >
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Answer: A: Blast Against Uniref90 Database Using Biopython?
... This is quite old, but if time / speed is an issue, [Diamond][1] is an accelerated BLAST aligner that is very fast. I've used it with a downloaded UniRef90 database and it works both for local testing & development (2015 Macbook Pro) as well as on the production servers. I can share code with yo ...
written 2.5 years ago by parism930
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Mapping between a NCBI protein and an UniProtKB protein from a FASTA file
... I have a FASTA file from using the BioPython BLASTp command programmatically. I want to map each of the entries to their associated UniProtKB (either Swiss or Trembl) (or even to a UniParc / Uniref if needed) entry. For an entry like the following, it seems there is no protein in UniProtKB. Is this ...
fasta sequence alignment blast written 2.5 years ago by parism930 • updated 2.5 years ago by darnells30
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Download UniProt databases via HTTP/HTTPS instead of FTP? (Google Apps Scripts Question)
... Hello, Does anyone know of a mirror to download the UniRef90 database via HTTP or HTTPS, or something supported by Google Apps Scripts? I want to download the [UniRef90 database](ftp://ftp.uniprot.org/pub/databases/uniprot/uniref/uniref90/), but it is not possible via FTP on Googgle Apps Scripts. [S ...
google sequence uniprot databases ftp written 2.6 years ago by parism930 • updated 2.6 years ago by me690
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Issue downloading files from FTP server to Ubuntu 16.04.2 VM (Azure)
... I am trying to download some data from the UniProtKB website. I have a Ubuntu 16.04.2 VM hosted on Azure. The main repository is hosted [here][1]. I want to download one of the .gz files, but when I use wget (wget "pathtofile") I have the following error: wget: unable to resolve host address ‘ftp. ...
wget ftp uniprot software error ubuntu written 2.7 years ago by parism930
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Improving the selection process of functional variants of an enzyme
... Hello! I'm working on the following problem. I are looking for enzymes of function X to clone into organisms. Currently, I use BLAST and then select several proteins that are similar and from distinct species and then order them, clone them, and test the organisms ability to do X. I'm looking for ...
protein function blast clustering written 2.7 years ago by parism930

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