Welcome to the DOTM SNP Discovery Site

This SNP detection tool allows users to search against PBI EST sequences generated from the DOTM project using blastn, and using match results along with the query sequence as input to the SNP prediction program Polybayes 3.0 (Copyright (C) 1998, 1999 Gabor T. Marth, Washington University, St. Louis, Missouri USA). The pipeline includes cleaning of the query sequence, and assembly of the matching sequences. The polybayes program utilizes tracefiles and quality values available for the EST sequences to make more acurate predictions of putitive snps. Results are returned as a report on p_snps detected, alignment profiles, as well as visualization of individual sequence trace files so that the user may validate individual p_snp sites.

Query Sequence Submission Form: Input reference sequence and parameters

Select a desired sequence file (FASTA format only)		OPTIONAL  Submit additional related sequences you wish to include in the search as a file (FASTA format only)
OR   paste a sequence into the text window below (FASTA fomat only)		OR   paste additional similar sequences into the text window below (FASTA fomat only)
Select Species Database: Brassica napus (169247 sequences) Brassica rapa (17096 sequences) Brassica carinata (1341 sequences) Brassica oleracea (13942 sequences) Brassica all (201636 sequences) None (Use only submitted related sequences)

Sequence Cleaning Options
Annotate:	Repeats Low complexity regions
Excise:	Vectors PolyA tail
Filter:	Ribos Yeast Ecoli RNA Chloro Mito

BLASTn Parameters
E-value Threshold
Mismatch Penalty (default = -3)
Match Reward (default = 1)

Assembly Parameters
Filter Input ~ Min Score
Filter Input ~ Max. E.value
Use DEFAULT assembly params	Yes No
Max. assembly overlap
Overlap similarity score cutoff
Min depth of coverage for repeats
Segment %sim threshold in clipping
Max. len. of contig end to clip
Max. len. of read end to clip
Max. len. of overhang after clip
Max sum of modified qscore clippable

SNP Detect Parameters
Polymorphic rates	Expected (coding region): [0-1]
	Paralogous: [0-1]
SNP Min. base quality	<100
Threshold SNP	[0-1]
Paralog filtering	On off

Output Options
Include:	Alignment Report Links to traceviewer
Mininum SNP Depth:	[Default: 4]
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