Medicago Sequencing Resources - CViT-blast utility

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Medicago Sequencing Resources - CViT-blast utility

- CViT-blast utility -

Blast a fasta-format sequence or set of sequences against the current Medicago truncatula psuedochromosome build. The output page will show two views of the blast hits: a compressed image, an expanded image that also shows BAC borders, and a table describing the hits. See the FAQs for more information.

For testing, here are some nucleotide and peptide sequences.

Instructions: choose a blast program and e-value, then paste your FASTA sequences.
Note: "Collapse HSPs within this range" applies to blastn and tblastn; see '?' for more information.

Genome build —

Blast type:	blastn tblastn blastp blastx	?
E-value: (e.g. 0.01 or 1e-6)		?
Collapse HSPs within this range: 0 = don't collapse; for nt targets only		?

Paste FASTA sequences: (Each query will be assigned a different color.)	OR	upload a FASTA file:

(May take some time. Please click the button only once.)

FAQs: What's a "pseudochromosome"? The pseudochromosomes are snapshots of genome sequence in chromosomes in the ongoing Medicago truncatula genome sequencing project. They consist of BAC sequences and sequence-contigs in approximate order, as determined by marker locations. The genome sequence for the euchromatic space is approximately half- to two-thirds completed, so there are many gaps, and BAC and contig orientations have not yet been determined. New pseudochromosomes are constructed weekly.; What are the little gray and black lines on the chromosome images? Black lines indicate sequence gaps; gray lines indicate boundaries between overlapping BACs (overlap has been removed in these cases).; What are the colored dots? Each dot represents a Blast HSP below the specified E-value. Several HSPs may correspond to one query sequence, so two dots don't necessarily indicate two independent matches of the same sequence.; What is CViT-blast? CViT stands for "Chromosome Visualization Tool." CViT is a set of perl and CGI scripts for flexibly visualizing features on chromosomes, and particularly for visualizing whole genomes. The scripts are still under development, but will be made publicly available when ready.

Credits:: CViT-blast: Atif Ahmed, Ethy Cannon and Steven Cannon (UMN).; Pseudochromosome construction by Shelley Wang (UMN) and Foo Cheung (TIGR).; All that sequence: the sequencing teams at University of Oklahoma, TIGR, Sanger Institute, and Genoscope.