how to extrtact the features of translation initiation site

Question

[jinxyhucy521]

I am doing the metagenomic gene prediction,and I want to extract features about translation initiation site,the Orphelia,Glimmer-MG,MetaProdigal have done some work about this,and I haven't got this features,has someone done the similar jobs?And I hope to get help from you !

Answer 1

[natasha.sernova]

There are some other tools.

Prokaryotes:

Prodigal: prokaryotic gene recognition and translation initiation site identification

https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-11-119

TICO: a tool for postprocessing the predictions of prokaryotic translation initiation sites

http://nar.oxfordjournals.org/content/34/suppl_2/W588.full

Tools for making and manipulating transcript centric annotations

https://www.bioconductor.org/packages/devel/bioc/manuals/GenomicFeatures/man/GenomicFeatures.pdf

Vertebrates:

A Novel Data Mining Approach for the Accurate Prediction of Translation Initiation Sites

http://lpis.csd.auth.gr/publications/Tzanis_ISBMDA06.pdf

Plants:

Dragon TIS Spotter: an Arabidopsis-derived predictor of translation initiation sites in plants

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3530916/

These posts as well:

This recent post for human genomes:

Get all the translation start site for human genome

These two are rather old, check if the links survived:

Initiation Codons: "Predictions" And "Alternative Initiation Codons"

Getting Blastx Translated Query