This page includes: sequence analysis, gene finding, multiple sequence alignment tools, and promoter analysis sites.

Sequence analysis:

• Double Twist (Doubletwist, INC) a "one-stop shop" for DNA sequence analysis -registration free but required

  Oakridge Computational Sciences multifunctional pages: GRAIL, Genome Channel (I haven't gotten the Genome Channel to work on Macs)

   

  Class at Caltech

   

  BLAST (Basic Local Alignment Search Tool) and other NCBI tools at NCBI: NCBI's sequence similarity search tool designed to support analysis of nucleotide and protein databases, which compares unidentified sequences with those in a database.

Gene finding:

List of Gene Finding Programs - list with links and description of methods. Includes some of the programs above plus others (GOOD SITE).

GeneBuilder: Excellent visualizations of results. This is from the Human Genome Project - some of it is very up to date and some parts of the site aren't. The presentation is great - just check with another gene finding program in addition to this one.

 

NEX: Gene finding program developed especially for Neurospora crassa by Judy Galbraith

 

FEX: The FEX (Find Exon) program initially predicts internal exons by linear discriminant function, evaluating open reading frames flanked by GT and AG base pairs (the 5' and 3' ends of typical introns). After internal exons are specified, 5' and 3' exons are predicted.

 

FGENE and FGENES: FGENE and FGENES rely on pattern recognition to predict exons, promoters and polyadenylation signals. Dynamic programming is used to specify the optimal combination of these features.

GeneMark.hmm: :The GeneMark.hmm algorithm is based on the prediction of exons using frame-dependent non-homogeneous Markov chain models. Also, the predictions of start codons are improved by the analysis of ribosome binding site patterns.

 

Glimmer - TIGR's gene identification program -Download

 

 

GRAIL: GRAIL (Gene Recognition and Assembly Internet Link) uses a number of sensor algorithms to evaluate coding potential (features including 6-mer composition, GC composition and splice junction recognition). The output of the sensor algorithms is input to a neural network, which used empirical data for training.

 

HMMGene: HMMGene uses a hidden Markov model to predict exons, splice sites and intergenic regions of vertebrate and C. elegans genes. The criterion of conditional maximum likelihood is applied.

ORFGene 2 and other programs for gene finding: ORFGene 2 first identifies potential exons and the encoded polypeptides, and then searches the SWISS-PROT database for homologous proteins. The closest homolog is used to define the coding region, in combination with conserved splice sites.

 

ORF Finder (NCBI)

 

MZEF-SPC (Michael Zhang's Exon Finder with Splice-Proximal Check) There are additional programs at the bottom of Michael Zhang's web page at CSHL.

 

Neurospora gene sequences to test

 

Multiple nucleotide or amino sequence alignment techniques are usually performed to fit one of the following scopes :  

• In order to characterize protein families, identify shared regions of homology in a multiple sequence alignment; (this happens generally when a sequence search revealed homologies to several sequences)
• Determination of the consensus sequence of several aligned sequences
• Help prediction of the secondary and tertiary structures of new sequences
• Preliminary step in molecular evolution analysis using Phylogenetic methods for constructing phylogenetic trees. 

ClustalW at EBI: Phylogenetic method for multiple sequence alignment. It compares overall sequence similarity of multiple sequences.

MSA2.1: optimal global alignment of < 8 sequences using dynamic programming at the Institute for Biomedical Computing. (protein only)

MEME: MEME (Multiple EM for Motif Elicitation) analyzes your sequences for similarities among them and produce a motif (highly conserved regions) for each pattern. It can also be used to search other sequences containing the MEME motifs using MAST. (both at San Diego Supercomputing Center, SDSC).

Block Maker: Block Maker finds conserved blocks in a group of two or more unaligned protein sequences, which are assumed to be related, using two different algorithms.

 

Promoter analysis

RSA: Regulatory Sequence Analysis Tools (originally for S. cerevisiae, now includes some bacterial genome sequences)

 

S. cerevisiae promoter database:

Michael Zhang's lab at Cold Spring Harbor

 

AlignACE George Church's lab at Harvard. Currently for procaryotic and Saccharomyces cerevisiae regulatory sequences

 

COMPEL http://compel.bionet.nsc.ru/ COMPEL collects information about composite regulatory elements (CEs) - pairs of closely situated sites and transcription factors binding to them. We define a composite element as a minimal functional unit within that both protein-DNA and protein-protein interactions contribute to a highly specific pattern of gene transcriptional regulation. The factors that cooperate at an individual CE mostly belong to different classes with respect to the structure of protein domains, namely DNA-binding and activation domain. The factors also differ in their functional properties: cell-specificity, inducibility and othres. Thus, composite regulatory elements contribute to the one of the fundumental principles of genom functioning - combinatorial nature of gene transcriptional regulation.

 

RegulonDB: a database on transcriptional regulation in Escherichia coli http://tula.cifn.unam.mx:8850/regulondb/regulon_intro.frameset > >>RegulonDB is a database on transcription regulation and operon organization in Escherichia coli. It describes regulatory signals of transcription initiation, promoters, regulatory binding sites of specific regulators, ribosome binding sites and terminators, as well as information on genes clustered in operons. These specific annotations have been gathered from a constant search in the literature, as well as based on computational sequence predictions. The genomic coordinates of all these objects in the E. Coli K-12

 

ATLAS: Several programs from SWMed for identification of exons and introns and forward and reverse primer identification

 

BCM Search Launcher at Baylor College of Medicine: Several alignment programs provided for both global and local alignments