Bioinformatics & Genomics
Genomics & DNA Sequence Analysis
DNA Sequence Analysis
Regulatory Site Finding
Repeat & Vector Masking
Sites with Multiple Tools
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BCM Gene Finder
[Baylor College of Medicine] This service provides several tools that use the identification of certain regions (splice sites, protein coding exons, promotor and poly-A regions) in nucleic acid sequences to find possible genes.
DNA sequence translation
[Virtual Genome Center] A program for identification of open reading frames in DNA sequences.
Eukaryotic Promoter Database
[DBGET] Database of eukaryotic promoter sequences.
[Univ. Montreal] A Unix C program used to find and translate ORFs. Flip reformats DNA sequences, and produces output files that can be used by other programs such as FASTA.
Gene Finding Programs
[University of Tokyo] A list of Gene Finding programs.
GeneFIND: Gene Family Identification Network Design
[Protein Information Resource] A database search system combining search/alignment tools and the ProClass database. Output includes global and motif scores, alignments to the best-matched members of the Pro-Site protein groups and PIR superfamilies, motif pattern matches, and links to the corresponding ProClass family records.
[Georgia Tech] This program is used for gene prediction in sequences. “The GeneMark program relies upon an Inhomogeneous Markov Model approach combined with training datasets to predict genes. Along with predicting genes, it can use RBS models to predict RBS sites and predict frameshifts.”
[University of Colorado] “GeneParser is a program for the identification of protein coding regions in genomic DNA sequences.”
[University of Pennsylvania] “GenLang is a syntactic pattern recognition system, which uses the tools and techniques of computational linguistics to find genes and other higher-order features in biological sequnce data. Patterns are specified by means of rule sets called grammars, and a general purpose parser, implemented in the logic programming language Prolog.”
[Stanford Univ.] A program designed to predict complete gene structures–including exons, introns, promoter and polyadenylation signals in genomic sequences. It differs from the majority of existing gene finding algorithms in that it allows for partial as well as complete genes and for the occurrence of multiple genes in a single sequence, on either or both DNA strands. The program is based on a probabilistic model of gene structure/compositional properties and does not make use of protein sequence homology information.
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[TIGR] “Glimmer is a system for finding genes in microbial DNA, especially the genomes of bacteria and archaea. Glimmer (Gene Locator and Interpolated Markov Modeler) uses interpolated Markov models (IMMs) to identify the coding regions and distinguish them from noncoding DNA.”
[Oak Ridge National Laboratory] A suite of tools designed to provide analysis and putative annotation of DNA sequences interactively and using automated computation. GRAIL supports e-mail and interactive graphical sessions.
HMMgene v. 1.1
[Center for Biological Sequence Analysis] A prediction server for genes in vertebrate and C. elegans.
Nucleotide Sequence Analysis
[Sanger Centre] A tool used for finding genes, promoters, poly-A, and splice sites in different organisms.
ORF: Open Reading Frame Finder
[NCBI] A graphical analysis tool which finds all open reading frames using standard or alternative genetic codes.
PROCRUSTES: Gene Recognition via Spliced Alignment
[Univ. of Southern California] (Gelfand, Mironov, Pevzner, Roytberg, Sing-Hoi Sze) Based on the spliced alignment algorithm, which explores all possible exon assemblies and finds the multi-exon structure with the best fit to a related protein, it uses related proteins and cDNAs for gene prediction.
[TIGR] RBSfinder is a
Perl script that
algorithm to find ribosome binding
sites for genes in bacterial and
archaeal genomes. It is normally run as
a post-processor to the Glimmer gene
finder or to other prokaryotic gene
[Iowa State University] “A method to identify potential splice sites in (plant) pre-mRNA by sequence inspection.”
[Institute of Advanced Biomedical Technologies] WebGene provides multiple tools for prediction and analysis of protein-coding gene structure.
[Sanger Center] A software package that compares DNA sequences at the level of conceptual translation, regardless of sequencing error and introns. It can compare a single protein or a profile HMM to a genomic DNA sequence, and predict a gene structure.
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