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NemaBLAST - Map your sequence to our various transcript database collections


Versus reads grouped by library

This selection is typically used to search for your sequence of interest amongst a custom selection of libraries from species of interest. For example, you may search your query against Trichinella spiralis cDNAs, but exclude all libraries except the adult libraries "Trichinella spiralis adult pAMP1 v1" and "Trichinella spiralis adult SL1 TOPO v1".

Select this option to align your nucleotide or protein sequence against databases comprising EST reads organized into their library of origin. After selection the organisms you would like to include, you will be given the chance to exclude specific libraries from the database. For information on specific libraries please use our Library Details page.
Versus transcript contigs, isotigs & genes

This selection is typically used to screen for the presence or absence of your query across a spectrum of organisms.

Select this option to align your nucleotide or protein sequence against databases comprising EST assembly contigs, gene CDS and/or transcript assembly isotigs organized by species. Databases in this set contain assembly contigs/isotigs constructed from different types of input data as well as CDS from final genesets. Each database can consist of contigs/isotigs built from input cDNA reads of several types or from CDS associated with finalized genesets. Names of the form "Acan_isotig11379" are isotigs constructed by a newbler assembly of Roche/454 cDNA data. Names in the form of "TS05971" are older contigs built from Sanger-sequencing based EST reads, typically assembled with Phrap. Names in the form of "CDS_Bmal|BM05276" are CDS of final genesets. Other naming formats that may appear indicate a contig and/or isotig that was imported from an external source, and may vary in their composition. For both Roche/454 and Sanger-sequence based assemblies as well as CDS genesets, the prefixes (first 4 letters for 454 data, and first 2 letters for Sanger data) indicate the species. For a list of these prefixes, please look in our NemaGene FAQ in the "Index of prefixes" section.

A Note on NemaBLAST

The NemaBLAST pages use WU-BLAST 2.0 (Gish, W. 1994-2002). Washington University BLAST (WU-BLAST) version 2.0 is a powerful software package for gene and protein identification, using sensitive and selective similarity searches of protein and nucleotide sequence databases. The feature list for WU-BLAST 2.0 is large, please visit http://blast.wustl.edu/ for more information on this software package

Please select what you'd like to BLAST against:


 
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