User: hpmcwill
hpmcwill • 1.1k
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I am currently working on a masters in Information and Library Studies. Previously I was a Software engineer for the Web Production team at the European Bioinformatics Institute (EMBL-EBI); a member of the team that supported, developed and maintained SRS at Lion Bioscience Ltd. and worked on genetic and genomic databases for Brassicas at the John Innes Centre.
Posts by hpmcwill
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... The FASTA suite also includes a set of sequence fragment search methods, which are optimised to handle the issues with short vs. long sequences. For the nucleotide case you will want to look at FASTM. For more info see PubMed:12096132, the FASTM service at EMBL-EBI, the FASTA guide and the documenta ...
written 4.7 years ago by
hpmcwill • 1.1k
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... First off... have you tried using the MS Windows binary as suggested by the authors (see http://clustal.org/omega/)? Note that the "INSTALL.txt" file is the version from the UNIX distribution (I am guessing that this was meant to be replaced), and all you should need to do is unpack the distribution ...
written 4.7 years ago by
hpmcwill • 1.1k
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... From the error messages it appears that the 'hybrid-plot-ng' component of UNAFold requires the GD library.
The GD library can be installed by:
A. Debian based Linux systems (e.g. Debian Linux, Ubuntu, Linux Mint, Bio-Linux, etc.)
sudo apt-get install libgd2-xpm
B. RedHat based Linux systems (e. ...
written 4.8 years ago by
hpmcwill • 1.1k
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... For large inputs ClustalW 2 can require very large amounts of memory. Since the distributed ClustalW 2 binary for MS Windows is 32-bit it can only use up to 2GB of memory before being terminated. So I am guessing your problem is likely to be memory usage.
So you have a couple of options:
A. Recomp ...
written 4.8 years ago by
hpmcwill • 1.1k
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... You may find this easier using the graphical version of ClustalW 2: ClustalX2 (see http://clustal.org/clustal2/), rather than the command-line ClustalW 2, FWIW the download for MS Windows is: clustalx-2.1-win.msi. After installation you will have a program menu item for ClustalX2, which you can run. ...
written 4.8 years ago by
hpmcwill • 1.1k
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... Try having a look at some of the transcription factor databases (e.g. JASPAR, TRANSFAC, etc.).
...
written 4.8 years ago by
hpmcwill • 1.1k
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Answer:
A: Downloading from MG-RAST
... The URL of the resource to be downloaded should generally be completely enclosed in quotes to prevent any of its contents being interpreted by the shell as additional arguments or file patterns. In your case this means something like the following will work as you expect:
cat names.csv | while rea ...
written 4.8 years ago by
hpmcwill • 1.1k
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... Given that the Legacy NCBI BLAST program 'blastpgp' was replaced with the 'psiblast' program in NCBI BLAST+, one possibility is that you are still using 'blastpgp', and thus the Legacy NCBI BLAST programs.
Check the command line being used, and ensure it has been converted to the form used by the N ...
written 4.8 years ago by
hpmcwill • 1.1k
2
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... Strictly 'nr' is non-identical not non-redundant. Other databases such as the UniProt UniRef databases provide non-redundant options.
Another consideration is that since BLAST uses a local alignment based search method it will find conserved local features (e.g. domains) as well as sequences which ...
written 4.8 years ago by
hpmcwill • 1.1k
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... From a bit of experimentation with 'xtract' it appears that the order of the command-line arguments is important, and thus a use of '-match' must be followed by an '-element' option. This appears to be the source of the error message you receive.
Using just 'xtract' the closest I've gotten so far i ...
written 4.8 years ago by
hpmcwill • 1.1k
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For A: Exhaustive up-to-date protein database?? nr?
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