New Species Genome BLAST and GBrowse

 

FlyBase is pleased to announce that we have developed a new interface for the community to query and view assembled and annotated versions of 11 of the sequenced Drosophila species:

 

D. anannassae, D. erecta. D. grimshawi, D. melanogaster, D. mojavensis, D. persimilis, D. pseudoobscura, D. sechellia, D. virilis, D. willistoni and D. yakuba.

 

You can access the 11 species from either the FlyBase BLAST page

 

http://flybase.bio.indiana.edu/blast/

 

or through the GBrowse window.

 

http://flybase.bio.indiana.edu/cgi-bin/gbrowse/dmel/

 

We have also provided a direct link between BLAST output and the GBrowse representation of the various species genomes and the relevant gene models/hit sites in the genome.

 

You will see that there are multiple tracks available on GBrowse for the newly represented species and these reflect the various annotation/gene model predictions from the labs that have provided each analysis (these can be clicked on or off as you wish) as well as GLEAN consensus sets of high confidence and those with lesser support called the "Exploratory Set". The GLEAN sets are provided as the default offering/response. We are also presenting a set of ortholog predictions computed in Mike Eisen's lab by Venky Iyer. These too appear as default. It is through these latter predictions that we offer a way to query the genomes from the GBrowse window.  Simply choose your species from the <Data Source> pull down menu and wait a few seconds for GBrowse to go to that genome.  Once there, type the Dmel gene symbol or CG##### of your choice into the <Landmark or Region> box and hit <Search>.  If an ortholog has been predicted you will be taken to its position in the genome.  If there is no predicted ortholog you will see a red-letter response <The landmark named XXX is not recognized. See the help pages for suggestions.> at the top of the page telling you this fact. 

 

A second way into the genomes is through the new BLAST.  Pick a gene and recover a FASTA file of its sequence.  Copy and Paste said sequence into the BLAST window and start the query.  Pick as many Drosophila species as you wish.  When your query is returned you will see the standard list of hits.  Pick one of the top hits and go to its specific record/alignment.  You will note that there is an html link on the Score line that reads "BLAST HIT on Genome Map". Click on this link and you will be taken to the position on the appropriate species genome wherein the hit resides.  The position of the hit will be highlighted in grey and this highlight will extend over as many of the evidence tracks as are open. The best hits should take you to the ortholog of your gene if there is one.  The lesser hits can take you to places in the genomes of the various species that are the residence of small bits of sequence similarity but not orthology.

 

Please be aware that these predictions are at this point preliminary and do not represent an official community consensus set of gene models.  We have released this preliminary set of analyses so that the community can have a look at what is there in the available genomes and begin some of their own forays into the wealth of data that are now available from the community genome sequencing projects.

 

FlyBase wishes to thank all of those who have contributed to the analyses to this point and to especially thank the NIH and the NIGRI for providing support for this project.

 

Please have a look and get back to us with problems or suggestions. 

 

The FlyBase Consortium.