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HomoloGene:
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News Briefs
Fly Genome Deposited
in GenBank
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LocusLink Adds Organisms and Search Fields |
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Two new organisms have been added to LocusLink: the zebrafish, Danio rerio, and the fly, Drosophila melanogaster. The data for Drosophila include all genes thus far identified in the recent deposition of the Drosophila genome. Links to the FlyBase database of Drosophila genome annotations are provided for these genes. Two new Boolean qualifiers have also been added to LocusLink. The first is termed “disease_known”, whereas the second is termed “has_seq”. These qualifiers provide the ability to search for records with associated diseases or sequence data. Together, these qualifiers can be used, for example, to determine how many disease genes have been sequenced using the search:
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GenBank Gets Billion Base Boost With Version 118.0 |
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GenBank release 118.0 is now available via FTP from NCBI. Uncompressed, the release 118.0 flat files require roughly 29,000 megabytes (MB) of disk space. The ASN.1 version of the GenBank sequence data requires roughly 24,000 MB. Release 118.0 comprises 8,604,221,980 base pairs, 7,077,491 sequences, and represents a growth of 1.23 billion base pairs over release 117.0. Pick up the latest GenBank at ftp://ncbi.nlm.nih.gov/genbank. |
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1.5 Million Bases of Bad Bug Sequenced |
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The complete 1.5 million base pair genomic sequence of the motile, gram-negative bacterium, Campylobacter jejuni (Feb 10, Nature), has been deposited in GenBank and can be viewed in Entrez Genomes. C. jejuni has earned a place in the FDA’s “Bad Bug Book” by being the bacterium most frequently associated with diarrhea in the United States. The Bad Bug is linked to 45% of diarrhea cases, leading Salmonella (30%), Shigella (17%), and E. coli (5%). Unchlorinated water and uncooked meat are the most common sources of contamination. Take a look at the genome on the NCBI Bacterial Genomics page at www.ncbi.nlm.nih.gov/PMGifs/Genomes/eub.html. |
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BLAST Version 2.0.13 is Released |
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The latest version of the BLAST suite of programs, version 2.0.13, is now available on the NCBI FTP site at ftp://ncbi.nlm.nih.gov/blast/. Archives of executables of standalone BLAST are found at this site within the “executable” directory. The BLAST network client is found within the “network” directory. The major enhancement of this release is that Bl2seq, the stand-alone version of the Web-based, BLAST2Sequences, can now perform nucleotide-protein (blastx style) comparisons. In this new version of Bl2seq, the “-p” option accepts the arguments “blastn”, “blastp”, or “blastx” rather than the Boolean “T” or “F” of prior versions. |
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