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4

I would recommend just downloading the database, which HUGO allows you to do free of charge. The HUGO website has a "downloads" tab at the top that takes you to the following page http://www.genenames.org/cgi-bin/statistics You will see a table of statistics relating to how many protein- or non-protein-coding genes there are catalogued, etc. Under the ...


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The group tries to predict possible epitope sequences for the generation of antibodies. This includes also non-linear epitopes where not all amino acids of the epitope are line up behind each other, but come in close contact due to a 3D-structure. To train their algorithm, they use data, where the boundaries of the epitopes and the non-epitopes are known and ...


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Found a tool: MUMmer is a system for rapidly aligning entire genomes. The current version (release 3.0) can find all 20 base pair maximal exact matches between two bacterial genomes of ~5 million base pairs each in 20 seconds, using 90 MB of memory, on a typical 1.8 GHz Linux desktop computer. If you know a better programmatic approach, let me know, ...


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You can try this: BLAST each sequence to every other sequence (pairwise). Every alignment (with some defined cutoff) denotes a connection. Map all connections. If a sequence is connected to some other directly or indirectly, it falls in a group. Put all the sequences that seq1 aligns to, in Group-1, then go to the alignments of these sequences; put all ...


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IMO irrespective of country and level (undergrad/Masters), if you can run a job on a High Performance Computing cluster or a supercomputer, you should mention that on your resume. And sure, you can use that in your statement, especially given the fact that not many have access to it, you had the rare opportunity and made full use of it. In my experience, I ...


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I'm not clear what "Locus", "Main locus", and "IGMT group" mean here exactly. Specifically, what is the difference between "Locus" and "Main locus"? From the same site: A locus is a set of IG or TR genes that are ordered and are localized in a same chromosomal location, in a given species. […] A locus comprises the genes of different ...


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Install bioconductor and use this library: http://www.bioconductor.org/packages/release/bioc/html/biomaRt.html You can access BioMart which lets you translate between different ID types


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Check out PGDSpider. The inputs and outputs table indicates that it supports conversion between FASTA and FSTAT formats, among many others.


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The PRANK and PAGAN algorithms have both come out of the Loytynoja lab in Finnland, and are stirring up the pot a bit. They use inferred phylogenetic relationships as a parameter, and tend to yield a much more 'gappy' alignment, supposedly due to more accurate handling of indels. For easy alignments the method doesn't matter so much, but if the sequences are ...


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I wouldn't expect different methods to give the same results. Further, why are you even testing non-normalized datasets, the results of that are completely and utterly useless for any purpose other than showing that normalization is important. In addition, an T-test is a special case of an ANOVA (and of course limma is itself using a moderated T-test, though ...


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You've picked a fascinating and very important organism to study. Unfortunately there are many many steps with many software packages that you'll need and each next step will depend on what you find making any particular tutorial nigh on pointless. I'm sorry to say that I don't think anyone will dump an entire project proposal or workflow as an answer. I'll ...


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There are couple of them. First if you want to sequence analysis basic packages are : http://www.bioconductor.org/help/workflows/high-throughput-sequencing/ Also, Maqweb seems promising. http://maqweb.sourceforge.net



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