HaploSNPer    allele and SNP detection tool

User Input  

Seed sequence (example) Other similar sequences (example)
Select a database (data info)

Select a sequence alignment program

Help

Related publications

Pre-processing of sequences

Remove vectors
Use Cross_match to remove vectors
Mask repeats
Use RepeatMasker to mask repeats

Parameters

BLAST / CAP3 and PHRAP
E-value
Similarity for CAP3 and PHRAP percent (must be > 65)
Haplotype construction
Similarity per polymorphic site [0..1]
Similarity over all polymorphic sites [0..1]
Low quality region
LQ length from 5'side nucleotides
LQ length from 3'side percent of the whole sequence
The weight value of LQ region [0..1]
SNP detection
Minimum cluster size sequences
Minimum redundancy of each allele sequences
Minimum confidence score [1..5]

Output format

Output format

Submit your job to HaploSNPer
Your e-mail address (optional):
(Output returned by email instead of waiting)           

© 2008 Laboratory of Bioinformatics, WUR

Last Modified March 23, 2009

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