Tracembler: software for in silico chromosome walks in unassembled genomes

PlantGDB

Tracembler

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Tracembler

Note: We are experiencing problems with Tracembler's link to NCBI's megablast program. We are working on correcting the problem, but in the meantime Tracembler is out of commission. Thanks for your patience. (August 25, 2010)

Tracembler allows you to do chromosome walks of trace sequences directly from NCBI's Trace Archive. This enables you to find your genes of interest in the most recent, pre-assembled sequence data. To use, please follow the steps below or . For further information, please see the help page or the examples page.

Step 1: Enter your email here:

Step 2: Paste your query sequences here (DNA or protein, in FASTA format) :

or upload your query from

Step 3: Select initial BLAST E-value to start walk:

Step 4: Select a target species to search:

Step 5:   or  



Advanced Parameters:

Tracembler
Number of rounds:
Round BLAST E-value:
Maximum number of BLAST queries:

Initial BLAST
Filters: Low Complexity Rodents Repeats Mask for lookup table only
Percent Identity (only relevant if your query is a nucleotide sequence):

Recursive nucleotide BLAST
Filters: Low Complexity Rodents Repeats Mask for lookup table only
Word-size:
Percent Identity:

Spliced Alignment
GenomeThreader species-specific splice site model:

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