Main logo
?
tutorial arrow
×
Submit new tools
Share tools covering the current topic. Provide easy-to-follow guidelines to improve their usability.
Share new tools with the community
Sign up for free to promote the availability of bioinformatics tools

Gene prediction software tools | RNA sequencing data analysis

Locating the protein-coding genes in novel genomes is essential to understanding and exploiting the genomic information but it is still difficult to accurately predict all the genes. The recent availability of detailed information about transcript…
G T A T C G C T A
CodingQuarry
Desktop

CodingQuarry

A highly accurate, self-training GHMM fungal gene predictor designed to work…

A highly accurate, self-training GHMM fungal gene predictor designed to work with assembled, aligned RNA-seq transcripts. RNA-seq data informs annotations both during gene-model training and in…

BLAST
Web
Desktop

BLAST Basic Local Alignment Search Tool

Allows to align query sequences against those present in a selected target…

Allows to align query sequences against those present in a selected target database. BLAST is a suite of programs, provided by NCBI, which can be used to quickly search a sequence database for…

G T A T C G C T A
BLASTX
Web

BLASTX Translated BLAST: blastx

Searches protein database using a translated nucleotide query. BLASTX is a…

Searches protein database using a translated nucleotide query. BLASTX is a BLAST search application that compares the six-frame conceptual translation products of a nucleotide query sequence (both…

G T A T C G C T A
RNAMiner
Web

RNAMiner

A multi-level bioinformatics protocol and pipeline. RNAMiner includes five…

A multi-level bioinformatics protocol and pipeline. RNAMiner includes five steps: Mapping RNA-Seq reads to a reference genome, calculating gene expression values, identifying differentially expressed…

G T A T C G C T A
PEP_scaffolder
Desktop

PEP_scaffolder

An efficient and fast genome scaffolding method, using proteins to scaffold…

An efficient and fast genome scaffolding method, using proteins to scaffold genomes. The pipeline aims to recover protein-coding gene structures. We tested the method on human contigs; using human…

G T A T C G C T A
BRAKER
Desktop

BRAKER

A pipeline for unsupervised RNA-seq-based genome annotation that combines the…

A pipeline for unsupervised RNA-seq-based genome annotation that combines the advantages of GeneMark-ET and AUGUSTUS. As input, BRAKER1 requires a genome assembly file and a file in bam-format with…

G T A T C G C T A
RNAsampleCDS
Web

RNAsampleCDS

Computes the number of RNA sequences that code user-specified peptides in one…

Computes the number of RNA sequences that code user-specified peptides in one to six overlapping reading frames. RNAsampleCDS can sample a user-specified number of messenger RNAs that code such…

G T A T C G C T A
GIIRA
Desktop

GIIRA Gene Identification Incorporating RNA-Seq data and Ambiguous reads

A gene prediction method that identifies potential coding regions exclusively…

A gene prediction method that identifies potential coding regions exclusively based on the mapping of reads from an RNA-Seq experiment. GIIRA was foremost designed for prokaryotic gene prediction and…

G T A T C G C T A
SnowyOwl
Desktop
Web

SnowyOwl

A gene prediction pipeline that uses RNA-Seq data to train and provide hints…

A gene prediction pipeline that uses RNA-Seq data to train and provide hints for the generation of Hidden Markov Model (HMM)-based gene predictions and to evaluate the resulting models. The pipeline…

G T A T C G C T A
TransDecoder
Desktop

TransDecoder

Identifies candidate coding regions within transcript sequences, such as those…

Identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome…

Related Websites
Information

By using OMICtools you acknowledge that you have read and accepted the terms of the end user license agreement.