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Halocaridina (HALO) rubra Basic Local Alignment Search Tool (BLAST)

Welcome to The Santos Lab implementation of the Basic Local Alignment Search Tool (BLAST) (Altschul et al. 1990, Journal of Molecular Biology 215:403-410) from NCBI for our Halocaridina rubra Holthuis, 1963 (Crustacea: Decapoda: Atyidae) transcriptomes. If you are unfamiliar with BLAST, click on the "?" button (upper right-hand corner) of the HALO-BLAST web page (link below) for a tutorial on the program(s). The transcriptomes utilized in these BLAST searches are from two (2) different lineages of Halocaridina and were assembled de novo with Trinity from Illumina Hi-Seq 2K data.  These searches are being run at the AU Dept. of Biological Sciences. Thus, once a search is started, results are returned nearly immediately. This work was partially funded by NSF-DEB #0949855.

 

As of September 2012, the number of contigs in the databases are:

EP (Windward Oahu lineage; Kahuku genetic group) Transcriptome:

60,635

EP (Windward Oahu lineage; Kahuku genetic group) Larval Transcriptome:

89,734

HILO (East Hawaii lineage; Puna genetic group) Transcriptome:

37,386

All three (3) Halocaridina rubra Transcriptomes:

187,755

 

Annotation has been done against the entire set of assembled contigs and filtered at a BLAST bit score of 100. A tab-delimited text file containing annotation information on these 46,267 contigs can be downloaded from here.

Statistics for these 46,267 contigs are:

Number of Contigs:

46,267

Total bp in Contigs:

68,342,661

Shortest Contig:

201 bp

Longest Contig:

15,565 bp

Ave. Length of Contigs:

1,477.1 bp

Median Length of Contigs:

1,164 bp

Average GC% of Contigs:

41.2%

 
>> Go to HALO-BLAST web page.

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