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Internet Resources

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.

[more info][10382]

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DNA sequence translation
[Virtual Genome Center] A program for identification of open reading frames in DNA sequences.

[more info][10390]

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Eukaryotic Promoter Database
[DBGET] Database of eukaryotic promoter sequences.

[more info][10983]

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[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.

[more info][11159]

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Gene Finding Programs
[University of Tokyo] A list of Gene Finding programs.

[more info][12039]

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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.

[more info][10449]

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[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.”

[more info][11163]

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[University of Colorado] “GeneParser is a program for the identification of protein coding regions in genomic DNA sequences.”

[more info][12032]

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[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.”

[more info][12031]

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[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.

[more info][10395]

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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.”

[more info][12035]

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[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.

[more info][10396]

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HMMgene v. 1.1
[Center for Biological Sequence Analysis] A prediction server for genes in vertebrate and C. elegans.

[more info][10397]

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Nucleotide Sequence Analysis
[Sanger Centre] A tool used for finding genes, promoters, poly-A, and splice sites in different organisms.

[more info][10403]

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ORF: Open Reading Frame Finder
[NCBI] A graphical analysis tool which finds all open reading frames using standard or alternative genetic codes.

[more info][10408]

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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.

[more info][10414]

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[TIGR] RBSfinder is a
Perl script that
implements an
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

[more info][14109]

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[Iowa State University] “A method to identify potential splice sites in (plant) pre-mRNA by sequence inspection.”

[more info][12038]

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[Institute of Advanced Biomedical Technologies] WebGene provides multiple tools for prediction and analysis of protein-coding gene structure.

[more info][12027]

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[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.

[more info][11287]

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