Gene Prediction

This section includes links to gene prediction programs for both eukaryotic and prokaryotic organisms. Resources that evaluate the available gene predicting programs are also included.

Found 43 links

Displaying 15 links

AGenDATool Content

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AGenDA is a web tool that compares the genomic sequences from evolutionarily related organisms in order to make gene predictions. It takes pairs of genomic sequences as input, aligns the sequences, and makes predictions based on splice signals, start and stop codons, and areas of conserved sequence.

links directory index: 11
TitlePublication YearGoogle Scholar Citation Count
AGenDA: gene prediction by cross-species sequence comparison200411

AMIGeneTool Content

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Annotation of MIcrobial Genes (AMIGene) is gene prediction server that can identify coding sequences in microbes.

links directory index: 70
TitlePublication YearGoogle Scholar Citation Count
AMIGene: Annotation of MIcrobial Genes200370

AnnotQTLTool Content

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AnnotQTL is a web tool for gathering functional and comparative information on a genomic region. It is designed to aggregate functional annotations from different websites by minimizing the redundancy of the information.

AUGUSTUSTool Content

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AUGUSTUS is a eukaryotic gene prediction tool. It can integrate evidence, e.g. from RNA-Seq, ESTs, proteomics, but can also predict genes ab initio. The PPX extension to AUGUSTUS can take a protein sequence multiple sequence alignment as input to find new members of the family in a genome. It can be run through a web interface, or downloaded and run locally.

This content is being maintained by Mario Stanke.

BAGELDatabase Content

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BActeriocin GEnome mining tooL (BAGEL) identifies putative bacteriocin ORFs (antimicrobial peptides) based on a database containing information about known bacteriocins and adjacent genes involved in bacteriocin activity.

links directory index: 48
TitlePublication YearGoogle Scholar Citation Count
BAGEL: a web-based bacteriocin genome mining tool200648

BAGEL2Tool Content

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BAGEL2 (BActeriocin GEnome mining tooL) identifies putative bacteriocins on the basis of conserved domains, physical properties and genomic context. Improved genome mining capacity from BAGEL.

links directory index: 16
TitlePublication YearGoogle Scholar Citation Count
BAGEL2: mining for bacteriocins in genomic data201016

BAGEL3Tool Content

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BAGEL3 is a web-server for automated identification of genes encoding bacteriocins and (non)-bacteriocidal post-translationally modified peptides using updated bacteriocin and context protein databases. Input is single or multiple FASTA formatted files.

links directory index: not available
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BLANNOTATORTool Content

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Blannotator is a rapid tool for functional prediction of gene or proteins sequences. The tool accepts DNA or protein sequences, given in FASTA-format, and performs a Blast homology search against UniProtKB databases. Matching sequences with similar annotations are merged into families of similar descriptions, which are, in turn, further unified, based on assigned GO-profiles retrieved from GOA, into sets of functionally equivalent sequences. As a result, a reliable description will be obtained.

This content is being maintained by mkankain.

links directory index: not available
TitlePublication YearGoogle Scholar Citation Count

BLASTTool Content

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Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families. A new BLAST report allows faster loading of alignments, has navigation aids and has improved usability.

DNAtoolsTool Content

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DNAtools include predicting DNA curvature; plotting physicochemical, statistical, or locally computed paramaters along DNA sequences; producing a 3-D model of a DNA sequence; searching an intron database.

links directory index: 65
TitlePublication YearGoogle Scholar Citation Count
DNA analysis servers: plot.it, bend.it, model.it and IS.200365

EvoCorTool Content

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EvoCor is a web server for predicting functionally related genes using phylogenetic and expression profiles.

links directory index: not available
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