Question

SNP annotation in non model animals

0

Entering edit mode

8.0 years ago

reza ▴ 300

hi every one

i get millions snp from NGS data (camel genome), now i would to annotate these variants

What way to do this, you recommend?

SNP next-gen • 2.0k views

ADD COMMENT • link updated 8.0 years ago by Biostar 20 • written 8.0 years ago by reza ▴ 300

0

Entering edit mode

Could be helpful if you mention the aim of your analysis and the type of annotation you aim to obtain.

ADD REPLY • link 8.0 years ago by WouterDeCoster 47k

0

Entering edit mode

i want to identify genic and intergenic snp, synonymous and non-synonymous snp and other annotation like this

ADD REPLY • link 8.0 years ago by reza ▴ 300

score 1 · Answer 1 · 2016-11-19

Look at these sources, they may be helpful.

Snpdat: easy and rapid annotation of results from de novo snp discovery projects for model and non-model organisms.

These authors (above) compare model and non-model organisms in terms of SNP-findings.

These papers below are about some camel research:

Genome sequences of wild and domestic bactrian camels

Identification of SNPs and their validation in camel (Camelus bactrianus and Camelus dromedarius)

Sequencing, Analysis, and Annotation of Expressed Sequence Tags for Camelus dromedarius

Estimating the Population Mutation Rate from a de novo Assembled Bactrian Camel Genome and Cross-Species

Comparison with Dromedary ESTs

The de novo genome assembly and annotation of a female domestic dromedary of North African origin