> > Gene Prediction

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.

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Found 30 links

Displaying 15 links

AGenDATool Content

http://bibiserv.techfak.uni-bielefeld.de/agenda/

DNA > Gene Prediction
Sequence Comparison > Analysis of Aligned Sequences

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.

NAR Web Server Issue 2004
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tagsanimals base sequence conserved sequence dna footprinting dna sequence analysis genes genomics humans mice nucleic acid sequence homology phylogeny rna splicing sequence alignment

AMIGeneTool Content

http://www.genoscope.cns.fr/agc/tools/amigene/Form/form.php

DNA > Gene Prediction
Model Organisms > Microbes

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

NAR Web Server Issue 2003
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tagsbacterial dna bacterial genes dna sequence analysis markov chains open reading frames

AnnotQTLTool Content

http://annotqtl.genouest.org

DNA > Annotations
DNA > Gene Prediction

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.

NAR Web Server Issue 2011
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AUGUSTUSTool Content

http://bioinf.uni-greifswald.de/augustus

DNA > Gene Prediction
DNA > Structure and Sequence Feature Detection
Expression > Splicing
Protein > Domains and Motifs

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.

NAR Web Server Issue 2004NAR Web Server Issue 2005NAR Web Server Issue 2006
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tagsadult algorithms alternative splicing animals artificial intelligence automated pattern recognition base sequence bile acids and salts cholic acids chromosome mapping computer simulation deoxycholic acid dna sequence analysis drosophila melanogaster exons female gene components gene expression genes genetic databases genetic models genetic variation genomics human genome humans hypercholesterolemia hyperlipidemias introns ldl lipoproteins male markov chains middle aged molecular sequence data proteins sequence alignment statistical models stochastic processes triglycerides vldl lipoproteins

BAGELDatabase Content

http://bioinformatics.biol.rug.nl/websoftware/bagel/bagel_start.php

DNA > Gene Prediction
Model Organisms > Microbes

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.

NAR Web Server Issue 2006
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tagsamino acid motifs bacterial genome bacteriocins genetic databases genomics multigene family open reading frames

BAGEL2Tool Content

http://bagel2.molgenrug.nl

DNA > Gene Prediction
Model Organisms > Microbes

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.

NAR Web Server Issue 2010
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tagsamino acid motifs anti-bacterial agents bacterial genome bacteriocins data mining genomics open reading frames

BLASTTool Content

http://www.ncbi.nlm.nih.gov/BLAST/

DNA > Gene Prediction
DNA > Sequence Retrieval and Submission
Protein > Sequence Retrieval
RNA > Sequence Retrieval
Sequence Comparison > Similarity Searching

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.

NAR Web Server Issue 2004NAR Web Server Issue 2006NAR Web Server Issue 2008
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tagsalgorithms amino acid sequence base sequence factual databases genetic databases genome humans mutation national library of medicine (u.s.) nucleic acid databases nucleic acid sequence homology nucleotides protein databases protein sequence analysis sensitivity and specificity sequence alignment sequence analysis systems integration united states
setsNational Center for Biotechnology Information (NCBI)

CPCTool Content

http://cpc.cbi.pku.edu.cn/programs/run_cpc.jsp

DNA > Gene Prediction
DNA > Structure and Sequence Feature Detection
RNA > Functional RNAs

CPC (Coding Potential Calculator) distinguishes protein-coding from non-coding RNAs based on the sequence features of the input transcripts.

NAR Web Server Issue 2007
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tagsanimals computational biology expressed sequence tags genetic code genetic transcription genetic variation genetic vectors messenger rna mice molecular sequence data nucleic acid databases protein biosynthesis proteins reproducibility of results rna

EUGENE'HOMTool Content

http://genopole.toulouse.inra.fr/bioinfo/eugene/EuGeneHom/cgi-bin/EuGeneHom.pl

DNA > Annotations
DNA > Gene Prediction
Model Organisms > Plants

EUGENE'HOM is a gene prediction software for eukaryotic organisms based on comparative analysis. The data is currently tuned for plant sequences of up to 400kb.

NAR Web Server Issue 2003
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tagsalgorithms complementary dna dna sequence analysis eukaryotic cells genes genome initiator codon nucleic acid sequence homology plant dna rna splice sites

FrameDTool Content

http://genopole.toulouse.inra.fr/bioinfo/FrameD/FD

DNA > Gene Prediction

FrameD is a program that predicts coding regions in prokaryotic and eukaryotic sequences that may contain frameshifts.

NAR Web Server Issue 2003
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tagsamino acid sequence homology bacterial genome complementary dna dna sequence analysis eukaryotic cells expressed sequence tags frameshift mutation gc rich sequence genes open reading frames

GeneFizzTool Content

http://pbga.pasteur.fr/GeneFizz/

DNA > Gene Prediction

GeneFizz is a tool for identifying genes using by using the physical characteristics of helix-to-coil transitions in DNA.

NAR Web Server Issue 2003
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tagsalgorithms animals biophysical phenomena biophysics computational biology dna dna sequence analysis drosophila melanogaster genes genetic code genetic models genetic techniques genomics molecular evolution nucleic acid conformation plasmodium falciparum protozoan dna protozoan genes protozoan genome

GeneMarkTool Content

http://opal.biology.gatech.edu/GeneMark/

DNA > Gene Prediction

The GeneMark family of programs employ Markov models and are specifically tuned for gene prediction for sequences from prokaryotes, viral genomes and eukaryotes.

NAR Web Server Issue 2005
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tagsalgorithms animals bacterial genes computational biology genes genomics humans markov chains viral genes

GeneSeqerTool Content

http://www.plantgdb.org/search/misc/PublicPlantSeq.php

DNA > Gene Prediction
Expression > Splicing
Model Organisms > Plants

GeneSeqer is a method to identify exon/intron structure by splice site prediction and spliced alignment in plant genomes.

NAR Web Server Issue 2003
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tagsarabidopsis complementary dna computational biology dna sequence analysis expressed sequence tags gene components genetic databases genetic transcription genomics nucleic acid repetitive sequences plant dna plant genes plant genome plant proteins plants protein sequence analysis sequence alignment

GenomeScanTool Content

http://genes.mit.edu/genomescan.html

DNA > Gene Prediction

Incorporates protein similarity information when predicting genes; based in part on GENSCAN.

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GENSCANTool Content

http://genes.mit.edu/GENSCAN.html

DNA > Gene Prediction

Identification of complete gene structures in genomic DNA.

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tagsanimals dna dna sequence analysis exons genes genetic models genetic promoter regions genetic techniques genetic transcription human genome humans introns markov chains molecular sequence data nucleic acid repetitive sequences probability protein biosynthesis proteins rna splicing vertebrates

Tags associated with subcategory 'DNA/Gene Prediction'

dna sequence analysis genomics humans algorithms animals genes computational biology sequence alignment base sequence genetic databases open reading frames proteins markov chains dna exons genetic models bacterial genome molecular sequence data nucleic acid sequence homology complementary dna expressed sequence tags human genome leghemoglobin rna reproducibility of results molecular models stochastic processes middle aged forecasting gc rich sequence conserved sequence chromosome mapping male base composition ldl lipoproteins histones initiator codon anti-infective agents archaeal genes bacterial genes archaeal genome automated pattern recognition vldl lipoproteins triglycerides evaluation studies as topic gene expression eukaryotic cells chemical dictionaries genome biomedical engineering predictive value of tests mice genetic transcription computer-assisted numerical analysis genetic techniques genetic promoter regions systems integration united states viral genome drosophila melanogaster factual databases protein biosynthesis rna splicing probability nucleic acid repetitive sequences insect genes sensitivity and specificity introns sequence analysis protein sequence analysis tata box hyperlipidemias rna polymerase ii reading frames molecular evolution mathematics neural networks (computer) statistical models synteny viral genes nucleotides protein databases ubiquitin secondary protein structure peptides proteome rna sequence analysis hypercholesterolemia vertebrates arabidopsis alcohol dehydrogenase data mining amino acid sequence homology amino acid sequence codon database management systems amino acid motifs mutation National Center for Biotechnology Information (NCBI) escherichia coli proteins genetic polymorphism