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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.
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As of September 2012, the number of sequences in the databases are:
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EP (Windward Oahu lineage; Kahuku genetic group) Transcriptome:
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60,635
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EP (Windward Oahu lineage; Kahuku genetic group) Larval Transcriptome:
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89,734
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HILO (East Hawaii lineage; Puna genetic group) Transcriptome:
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37,386
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All three (3) Halocaridina rubra Transcriptomes:
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187,755
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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:
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Number of Contigs:
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46,267
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Total bp in Contigs:
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68,342,661
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Shortest Contig:
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201 bp
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Longest Contig:
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15,565 bp
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Ave. Length of Contigs:
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1,477.1 bp
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Median Length of Contigs:
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1,164 bp
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Average GC% of Contigs:
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41.2%
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