| Please select genome and dbSNP version: |
|
| Please insert a region coordinates, paste sequence or select input file: |
Chromosome: Start position: End position:
or paste sequence below:
Allowed characters in sequence: A,C,G,T,N,a,c,g,t,n. Other characters are converted to N. Numbers and blanks are ignored. FastA format is allowed.
or select Your input file in FastA format (plain .txt file only!): |
| Mask SNPs with symbol: |
With 'N' symbol (default)
With lower-case letter
With IUPAC symbol
With custom symbol -> |
| Mask SNPs based on major/minor allele frequency (HUMAN ONLY!): |
Replace with upper-case letter using HapMap3 major allele frequency
Replace with lower-case letter using HapMap3 major allele frequency
Population:
HapMap3 major allele frequency cutoff: %
HapMap3 major allele callrate cutoff: %
|
| Mask SNPs based on heterozygosity or validation: |
Global minor allele frequency (MAF):
(0-0.5 eg. 0.497)
Heterozygosity of a SNP:
(0-0.75 eg. 0.1)
SNP validation info:
|
| Repeat-masking options: |
GenomeMasker options: |
GenomeMasker with lower-case letters (default)
GenomeMasker with custom letter ->
RepeatMasker with lower-case letters
NO repeat-masking |
BOTH strands (default)
FORWARD strand only
REVERSE strand only
Outside TARGET region
This type masks upper strand in front of target region and lower strand behind the target region. FROM and TO define start and end nucleotides of the target region (NOT an absolute positions in chromosome!).
From: to:
Number of bp to mask:
(from 3' end of repeats)
|
| If you enter Your email address, You will get an email when SNPmasker job is finished (optional): |
|
| |
