Tip of the Week: PhylomeDB

1 December, 2010 (09:00) | Tip of the Week | By: Trey

Gene phylogenies (as opposed to species phylogenies) can be very useful in determined gene function, history, orthology and paralogy predictions. PhylomeDB (link added!) is a database of gene phylogenies (or as they call them, Phylomes.. no end to the ‘omes is there? :) . Currently there are over a dozen such phylomes from species like humans and yeast. The database allows you to obtain phylogenies of genes based on gene ID or BLAST, you can also get orthology predictions and alignments and more. Today’s tip is introducing you to the database.

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Comments: 4

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Pingback from Tweets that mention Tip of the Week: PhylomeDB | The OpenHelix Blog — Topsy.com
Time December 2, 2010 at 9:28 AM

[...] This post was mentioned on Twitter by Wess, Andrew Kwon. Andrew Kwon said: Tip of the Week: PhylomeDB http://j.mp/hXB0u2 [...]

Comment from Toni Gabaldon
Time December 2, 2010 at 11:20 AM

Cool tutorial, it is really useful for us.

Regarding the term “phylome”, it was not coined by us. It was defined by Sicheritz-Pontén and Siv Andersson in 2001 (NAR 29(2):545-52.) as the full complement of trees for all the genes encoded in a genome.

We considered it a useful term, since it does not refer to any large collection of phylogenetic trees, but rather to the collection of trees reconstructed from every gene encoded in a reference (or seed) genome. This distinction is important for applications aiming at truly genome-wide scales.

Hope this helps.

Cheers, Toni

Comment from Trey
Time December 2, 2010 at 12:05 PM

Glad you liked it Toni. I was pleased to have found PhylomeDB, nice tool.

I do see the utility of the term as it does set apart truly genome-wide scaled data, just surprises me how often ‘ome’ can and is used. Thanks for the 2001 NAR article, phylome actually seems to be an early coinage in the ‘ome’ world. I think it’d be interesting to see a history of the suffix :) ..

Pingback from Tip of the Week: MetaPhoOrs, orthology and paralogy predictions | The OpenHelix Blog
Time March 30, 2011 at 1:07 AM

[...] researchers and developers at PhylomeDB haven’t rested on their laurels. I did a tip of the week on PhylomeDB 3 months ago and not too long ago I was checking over there and found the team had created another [...]