常用Motif预测软件

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所属分类:Bioinformatics

ELPH is a general-purpose Gibbs sampler for finding motifs in a set of DNA or protein sequences. The program takes as input a set containing anywhere from a few dozen to thousands of sequences, and searches through them for the most common motif, assuming that each sequence contains one copy of the motif. ELPH has been to find patterns such as ribosome binding sites (RBSs) and exon splicing enhancers (ESEs).

PROSITE Search Form Allows you to rapidly compare a protein sequence against all patterns stored in the PROSITE pattern database. ScanProsite: Protein against Prosite form allows one to scan a protein sequence (either from SWISS-PROT or provided by the user) for the occurrences of patterns sorted in the PROSITE database. Pattern against SWISS-PROT scans in all of the SWISS-PROT database (including weekly releases) for the occurrence of a pattern that can originate from PROSITE or be provided by the user. (ExPASY)

Motifs in protein databases program determines if a protein motif is present in a database of protein sequences. This program allows the user to define a protein motif and then determine if a DNA sequence might encode them or if they are present in a protein database. The programs do not search a library of predefined protein motifs. A motif is defined by entering the amino acids of interest at each position.(Alces)

MatInspectorA tool for the detection of transcription factor binding sites. It is able to locate matches of sequences of unlimited length and compare one, several or all sequences in a sequence file against all or selected subsets of matrices from a library of matrix descriptions of protein binding sites. (GSF)

MEME Multiple EM for Motif Elicitation system allows one to discover motifs of highly conserved regions in groups of related DNA or protein sequences and search sequence databases using motifs using MAST: Works by calculating match scores for each sequence. The match scores are converted into various types of p-values and these are used to determine the overall match of the sequence to the group of motifs.(SDSC) 

Regular Expression Searches of Sequence DB using FPAT. This page is designed to search a molecular sequence database (proteins only) for patterns using simple regular expressions.At present, only protein sequence databases are available on the server. (Univ. of Toronto)

BCM Search Launcher : The Baylor College of Medicine has a variety of biology related search and analysis services including general protein sequence/Pattern searches and Species-Specific Protein Sequence Searches.(HGSC)

Screening pattern or alignment against PROTEIN databank : This method of looking for all pattern entries in PROTEIN databank is almost the same as in PROSITE screening procedure. The one difference is that coincidence of pattern's and fragment's letter could be seen in a broad sense: as a similarity of letters according to a weight matrix selected by the user. (genebee) 

Pattern Searching Proteins A collection of software tools for protein sequence analysis. PATTINPROT scans a protein sequence or a protein database for one or several patterns. PROSCAN scans a protein sequence for sites/signatures against the PROSITE database. 

PPSEARCH : Prosite Database Searches (sequence against databases of motifs). Allows you to search sequences for motifs or functional patterns in the prosite database (EBI)

COGnitor: Compare your sequence to COG- Clusters of Orthologous Groups database. Each COG consists of individual proteins or groups of paralogs from at least 3 lineages and thus corresponds to an ancient conserved domain. (NCBI)

HMMER Sean Eddy: Profile hidden Markov models can be used to do sensitive database searching using statistical descriptions of a sequence family's consensus.The advantage of using HMMS is that HMMS have a formal probabilistic basis and can be trained from unaligned sequences, if a trusted alignment isn't yet known. They do however make poor models of RNAs because they cannot describe base pairs. HMMER is a freely distibutable implementation of profile HMM software for protein sequence analysis. (Washington Univ.)

emotif is a research system that forms motifs for subsets of aligned sequences. Emotif ranks the motifs that it finds by both their specificity and the number of supplied sequences that it covers.(Stanford Bioinformatics Group)

FunSiteP Promoter Recognition: Recognition and classification of eukaryotic promoters by searching transcription factor binding sites using transcription factor binding site consensi. (GSF)

SMART Simple Modular Architecture Research Tool: Allows rapid identification and annotation of signalling protein domain sequences. It is able to determine the modular architectures of single sequences or genomes. (EBI)

SAM : Sequence Alignment and Modeling System using HMM (Hidden Markov Model). SAM is a collection of software tools for creating, refining and using linear HMM for biological sequence analysis. Documentation for SAM can be found here.(Pasteur)

BioRainbow : Human Promoter Extractor (Prom Extra). The Promextra windows application is designated to solve the problem of extracting promoters fast and simple for given list of genes

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