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Thursday, May 30, 2013

Genome browsers

If you are doing research in biology, you will have to know how to use the Genome browsers:
UCSC genome browser, Ensemble, and the NCBI genome browser.

See a introduction here:

I use UCSC genome browser a lot, mostly because of the rich annotation tracks. Sometimes, I go to Ensemble, it has a better view of sequences of exons and introns etc. I barely use the NCBI genome browser.

For Next Generation Sequencing analysis, you will be using some local genome browsers

IGV from Broad Institute

SeqMonk , it is excellent for some quantitation analysis of ChIP-seq, RNA-seq data.

it is really good for motif analysis besides the genome browsing function.

IGB, I have not used it personally

other browsers like Gbrowser
 from the GMOD project is also an alternative.

Artemis from sanger Institute:

see a wiki link here:

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