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Ab initio gene detection software tools | Gene expression data analysis

Ab initio gene prediction in transcripts has rarely been addressed compared to gene prediction on the genomic level. At the time of Sanger sequencing, annotation of Sanger transcripts (ESTs) was frequently done by alignment based methods as well as…
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Prodigal
Desktop

Prodigal PROkaryotic DYnamic programming Gene-finding ALgorithm

A gene-finding program for microbial genomes. The goals of Prodigal were to…

A gene-finding program for microbial genomes. The goals of Prodigal were to attain greater sensitivity in identifying existing genes, to predict translation initiation sites more accurately, and to…

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GeneMarkS-T
Desktop

GeneMarkS-T

A tool for ab initio identification of protein-coding regions in RNA…

A tool for ab initio identification of protein-coding regions in RNA transcripts. The algorithm parameters are estimated by unsupervised training which makes unnecessary manually curated preparation…

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OrfPredictor
Web

OrfPredictor

A web server designed for identifying protein-coding regions in expressed…

A web server designed for identifying protein-coding regions in expressed sequence tag (EST)-derived sequences. For query sequences with a hit in BLASTX, the program predicts the coding regions based…

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ESTScan
Desktop
Web

ESTScan

A program that can detect coding regions in DNA/RNA sequences, even if they are…

A program that can detect coding regions in DNA/RNA sequences, even if they are of low quality (e.g. EST sequences). ESTScan will also detect and correct sequencing errors that lead to frameshifts.

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AlignWise
Desktop

AlignWise

Combines Genewise with our own homology-based method, AlignFS, to identify…

Combines Genewise with our own homology-based method, AlignFS, to identify protein-coding regions and correct erroneous frame-shifts, suitable for subsequent phylogenetic analysis. We compared…

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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…

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