domingo, novembro 09, 2008

ferramentas cientificas Online By Dr O.lverkall

Análises estruturais


VAST Search at NCBI - VAST Search is NCBI’s structure-structure similarity search service. It compares 3D coordinates of a newly determined protein structure to those in the MMDB/PDB database.

PDB - Protein Data Bank. The single worldwide repository for the processing and distribution of 3-D biological macromolecular structure data.

The PredictProtein Server

MFOLD - RNA and DNA folding package developed by Dr. Michael Zuker.

ToPLign

IUCr - International Union of Crystallography


ferramentas cientificas Análises de domínios e motivos

Análises de domínios e motivos


Pfam - Pfam is a large collection of multiple sequence alignments and hidden Markov models covering many common protein families. Pfam version 16.0 (November 2004) contains alignments and models for 7677 protein families, based on the Swissprot 44.5 and SP-TrEMBL 27.5 protein sequence databases.

BLOCKS - at the Fred Hutchinson Cancer Research Center Blocks WWW server. Search your protein or DNA sequence against a Blocks Database.

eBLOCKS - database of protein sequence blocks — ungapped alignments of highly conserved regions among a protein family or superfamily.

eMOTIF - collection of more than 170000 highly specific and sensitive protein sequence motifs representing conserved biochemical properties and biological functions.

PROSITE - The ScanProsite tool allows to scan protein sequence(s) (either from Swiss-Prot or TrEMBL or provided by the user) for the occurrence of patterns, profiles and rules (motifs) stored in the PROSITE database, or to search protein database(s) for hits by specific motif(s). The program PRATT can be used to generate your own patterns.

ProDom - The Protein Domain Database. Is a comprehensive set of protein domain families automatically generated from the SWISS-PROT and TrEMBL sequence databases.

PatScan - PatScan is a pattern matcher which searches protein or nucleotide (DNA, RNA, tRNA etc.) sequence archives for instances of a pattern which you input.

ferramentas cientificas analises metabólicas

Análises Metabólicas


KEGG - Kyoto Encyclopedia of Genes and Genomes, as part of the research projects in the Kanehisa Laboratory of Kyoto University Bioinformatics Center.

Metabolic Design and Genome Analysis at Integrated Genomics - Genome structures, annotated genomes, their encoded metabolism, comparative pathway analyses, and more, are available for licensing.

Boehringer Mannheim, Biochemical Pathways - This page gives access to the digitized version of the Roche Applied Science “Biochemical Pathways” wall chart.

Bioinformatics Group at MCS ANL Projects - High throughput comparative and evolutionary analysis of Genomes and metabolic networks with Grid computational backend. PUMA2 - a system for High-throughput analysis of genomes and metabolic reconstructions from the sequence data. Currently PUMA2 contains 1034 genomes and allows interactive analysis of the sequence data using a variety of bioinformatics tools.

ferramentas cientificas Codificantes

análises de genes e regiões codificantes


GeneMark - A family of gene prediction programs provided by Mark Borodovsky’s Bioinformatics Group at the Georgia Institute of Technology, Atlanta, Georgia.

OMIM - Online Mendelian Inheritance in Man

Unigene - UniGene is an experimental system for automatically partitioning GenBank sequences into a non-redundant set of gene-oriented clusters.

LocusLink - LocusLink provides a single query interface to curated sequence and descriptive information about genetic loci. It presents information on official nomenclature, aliases, sequence accessions, phenotypes, EC numbers, MIM numbers, UniGene clusters, homology, map locations, and related web sites.

ORF Finder at NCBI - The ORF Finder (Open Reading Frame Finder) is a graphical analysis tool which finds all open reading frames of a selectable minimum size in a user’s sequence or in a sequence already in the database.

SRS - Sequence Retrieval System. Network Browser for Databanks in Molecular Biology

DeCypher - Bioinformatics Supercomputer. The TimeLogic DeCypher system dramatically accelerates computationally intensive bioinformatics algorithms—including BLAST, Smith-Waterman, and HMM analysis. Its amazing calculation speed is achieved through a combination of innovative hardware and software engineering.

ferramentas científicas analise genês
GeneMark - A family of gene prediction programs provided by Mark Borodovsky’s Bioinformatics Group at the Georgia Institute of Technology, Atlanta, Georgia.

OMIM - Online Mendelian Inheritance in Man

Unigene - UniGene is an experimental system for automatically partitioning GenBank sequences into a non-redundant set of gene-oriented clusters.

LocusLink - LocusLink provides a single query interface to curated sequence and descriptive information about genetic loci. It presents information on official nomenclature, aliases, sequence accessions, phenotypes, EC numbers, MIM numbers, UniGene clusters, homology, map locations, and related web sites.

ORF Finder at NCBI - The ORF Finder (Open Reading Frame Finder) is a graphical analysis tool which finds all open reading frames of a selectable minimum size in a user’s sequence or in a sequence already in the database.

SRS - Sequence Retrieval System. Network Browser for Databanks in Molecular Biology

DeCypher - Bioinformatics Supercomputer. The TimeLogic DeCypher system dramatically accelerates computationally intensive bioinformatics algorithms—including BLAST, Smith-Waterman, and HMM analysis. Its amazing calculation speed is achieved through a combination of innovative hardware and software engineering.

ferramentas científicas

Análise e Comparação de Seqüencias

BLAST at NCBI

ClustalW at EMBL - Clustal W is a general purpose multiple sequence alignment program for DNA or proteins.It produces biologically meaningful multiple sequence alignments of divergent sequences. It calculates the best match for the selected sequences, and lines them up so that the identities, similarities and differences can be seen. Evolutionary relationships can be seen via viewing Cladograms or Phylograms.

FASTA

Promoter Prediction by Neural Network - Our training and test sets of human and Drosophila melanogaster promoter sequences are available to the community for testing transcription start site predictors. These sites also contain our representative, standardized data sets of human and Drosophila melanogaster genes.

SAM - Sequence Alignment and Modeling System

ToPLign

Multiple Sequence Alignment at HGSC

VSNS - BioComputing Division Multiple Alignment Resource Page. This page was developed for the GNA-VSNS Biocomputing course.

Links to On Line Analysis Tools at ABIM

RefSeq - The Reference Sequence (RefSeq) collection aims to provide a comprehensive, integrated, non-redundant set of sequences, including genomic DNA, transcript (RNA), and protein products, for major research organisms.

dBEST - dbEST is a division of GenBank that contains sequence data and other information on “single-pass” cDNA sequences, or Expressed Sequence Tags, from a number of organisms.

PHRAP - phrap is a program for assembling shotgun DNA sequence data.

SRS - Sequence Retrieval System. Network Browser for Databanks in Molecular Biology

DeCypher - Bioinformatics Supercomputer. The TimeLogic DeCypher system dramatically accelerates computationally intensive bioinformatics algorithms—including BLAST, Smith-Waterman, and HMM analysis. Its amazing calculation speed is achieved through a combination of innovative hardware and software engineering.









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