Sequence Related Sites

Protein/Nucleic Acid Sequence Search Sites

A B C D E F G H I J K L M

N O P Q R S T U V W X Y Z

3D_ali is a database of aligned protein structures and related sequences at EMBL-Heidelberg (Updated 5/1/99).

	AA Analysis - Protein and Amino Acid Identification in SwissProt and PIR using Amino Acid Composition at EMBL-Heidelberg. (Updated 4/8/99)
	AA CompIdent - is a tool which allows the identification of a protein from its amino acid composition using SWISS-PROT and / or TrEMBL databases at the ExPASy, Switzerland Molecular Biology Server. (Updated 4/8/99)
	AA CompSim - is a tool which allows the comparison of the amino acid composition of a SWISS-PROT entry with all other SWISS-PROT entries so as to find the proteins whose amino acid compositions are closest to that of the selected entry at the ExPASy, Switzerland Molecular Biology Server. (Updated 4/8/99)
	ALIGN - Optimal Global Alignment of Two Sequences

Alternatives	Location	Comments
GeneStream	GeneStream	None Available
MIPS	MIPS, Germany	Server Down 4/8/99

	AbCheck - Test an Antibody Sequence Against the Kabat Database at Department of Biochemistry and Molecular Biology University College London, UK (Updated 4/8/99).
	ALIGN - Optimal Global Alignment of Two Sequences with No Short-cuts at Genestream, Montpellier, France (Updated 5/2/99).

Alternatives	Location	Comments
ALIGN	Genestream, Montpellier, France	Optimal Global Alignment of Two Sequences with No Short-cuts
LALIGN	Genestream,Montpellier, France	Calculates the N-Best Local Alignments Between Two Sequences

Aligner (see MBS-aligner)

AllAll - Relationships in a Set of Related Peptides at ETH-Z�rich, Switzerland. options: PamData: estimates of pam distances and variances, PhyloTree: unrooted phylogenetic tree, RootedTree: rooted phylogenetic tree, 2DPlacement: placement of sequences in the plane,SplitData: values of dSplits, SplitGraph: graph visualizing dSplits, MulAlignment: Multiple alignment, ProbAncestral: Probabilistic ancestral sequence, KWIndex: Kabat-Wu variation index, ProbIndex: probability variation index, ScaleIndex: maximum likelihood variation index, SIAPrediction: prediction of Surface/Interior/Active site,ParsePrediction: prediction of parse regions (updated 4/8/99)

AllAllDB: Querying the all-against-all database of SwissProt at ETH-Zurich,Switzerland (Updated 4/8/99)

	Baylor College of Medicine (BCM) Search Launcher is an on-going project to organize molecular biology-related search and analysis services available on the WWW by function by providing a single point-of-entry for related searches at the Human Genome Sequencing Center Baylor College of Medicine (Updated 5/1/99).
	Bioccelerator is a protein sequence database search tool at European Bioinformatics Institute (server down 5/22/99)(Updated 5/1/99).
	BioSCAN is an attempt to provide a novel, powerful computational tool to molecular biologists for rapid search and analysis of biological sequences at the UNC-Chapel Hill (Updated 5/1/99)

	Boxshade (Ver. 3.2, Online version) Pretty Printing and Shading of Multiple-Alignment files (Updated 10/03/01).
	Blast- Basic Local Alignment Search Tool. Table Below lists various Blast mirrors (Updated 4/4/99)

Alternatives	Location	Comments
Blast NCBI	NCBI	Covers a Wide Range of Databases; Advanced and Basic Searches are possible
Blast Genomenet	Genomenet	Somewhat limited in the range of the databases.
Blast, Montpellier	GeneStream	I like this one the best because it seems to be very comprehensive and easy to use
Blast at Baylor	Baylor College of Medicine	It uses the same server as NCBI. I think that it is relatively old.
Blast Enhanced BCM Launcher	Baylor College of Medicine Search Launcher	Provides a single point of entry for a search of a variety of different protein/nucleic acid sequence databases.
BlastPat	Baylor College of Medicine Search Launcher	BLAST-based Pattern Database Search. Note: As of 5/1/99, It was being updated.

	BlastPat BLAST-based Pattern Database Search. Note: As of 5/1/99, It was being updated. at the Baylor College of Medicine Search Launcher (Updated 5/1/99)
	Blocks automatically looks for the most highly conserved regions in groups of proteins at the Fred Hutchinson Cancer Research Center, Seattle, WA (Updated 5/1/99).

	CLUE is a collection of useful links for molecular biology related material at Genomenet, Japan (Updated 5/2/99).
	CLUSTALW (server down 5/22/99) Multiple Sequence Alignment Tool at European Bioinformatics Institute (EBI) (Updated 5/1/99).
	Codon Usage - Analysis of Different ORFs in a Gene Sequence at University of Minnesota (Updated 5/2/99). (See DNA Sequence Translation.)

	Darwin, a Computational Biochemistry Research Tool: Darwin stands for Data Analysis and Retrieval With Indexed Nucleotide/peptide sequences. An interactive tool for peptide and nucleotide sequence analysis at ETH, Zurich, Switzerland.
	dbEST database of "Expressed Sequence Tags" at The National Center for Biotechnology Information (Updated 5/1/99).

	DBGET/LinkDB is a simple database retrieval system for finding and obtaining specific entries of diverse databases at Genomenet WWW server, Japan (Updated 5/2/99)
	DNA Sequence Translation provides an interface to a program for identification of open reading frames in DNA sequences at the Alces Server , U. Minnesota (Updated 5/1/99).

	Dot Plots is a very fast dot plot algorithm designed for large DNA sequences at Alces WWW Server (Updated 5/1/99).
	DOTS is a database of clustered and assembled partial gene sequences (ESTs) and mRNA sequences from human and mouse at the University of Pennsylvannia (Updated 5/3/99).

	E. Coli Cell Envelope Database (ECCE), the database is comprised of Proteins of the Inner Membrane, Periplasmic Proteins, and the Proteins of the Outer Membrane at Cardiff University (Updated 6/16/200)
	E. Coli Database Collection (ECDC) provides all the information regarding the entire E.Coli K12 chromosome at Justus- Liebig-University (Updated 5/1/99).
	EMBL- simple sequence retrieval system by Accession Number at EMBL, Heidelberg (server down 5/22/99) (Updated 5/1/99).
	Enzfinder (see MBS-Enzfinder) (Updated 6/16/99).
	Enzyme Data Bank contains the recommended name, catalytic activity, etc. for each type of characterized enzyme for which an EC number has been provided at the Maize Genome Database (5/22/99)

FASTA3 Compare a Nucleic Acid Sequence to Nucleotide Sequence Databases at the European Bioinformatics Institute (EBI, server down 5/22/99)(Updated 5/1/99).

Alternatives	Location	Comments
FASTA3	EBI	provides a slick looking interface to fasta
FASTA, Genomenet	Genomenet	Fasta Alternative
FASTA, Montpellier	GeneStream	Useful alternative to the FASTA3
FAST-PAT/FAST-SWAP	BCM Search Launcher	Fasta based Pattern Database Search
LFASTA	GENESTREAM	Local Similarity Searches Between Two Sequences Showing Local Alignments
TFASTA	GENESTREAM	Match a Protein Sequence Against All Six Frames of GenBank Sequences

FAST-PAT/FAST-SWAP is a Fasta-based Pattern Database Search at the Baylor College of Medicine (BCM) Search Launcher (Updated 5/1/99).

gdb, the human genome database is an international collaboration in support of the human genome project at the Johns Hopkins University Bioinformatics Webserver (Updated 5/2/99). Note: the site at Hopkins might be temporarily terminated

Alternatives	Location	Comments
gdb	Johns Hopkins	Main Server
various	various

	GenBank is the NIH's database of all known nucleotide and protein sequences including supporting bibliographic and biological information. This is a mirror site at EMBL, Heidelberg. (Updated 5/2/99).
	GeneCards is a database of human genes, their products and their involvement in diseases at the Weizmann Institute of Science (Updated 5/1/99).
	Gene Finder - Predict Gene Structure, Internal Exons and Splicing Sites in DNA and Exon-Exon Junction in cDNA at the Baylor College of Medicine (Updated 5/22/99).
	Genequiz is an automated analysis of biological sequences. Analysis of the complete genomes of yeast, Methanococcus jannaschii, Haemophilus influenzae, Mycoplasma genitalium. The server is at European Bioinformatics Institute EBI ( server down 5/22/99 ) (Updated 5/22/99).
	GenLang - Find Genes and Other Higher-Order Features in Nucleotide Sequences (RNA/DNA) at CBIL, University of Pennsylvania (Updated 5/2/99).

	G protein-coupled receptor database (GBCRDB) at EMBL, Heidelberg (Updated 5/1/99).
	Grail - Analysis of the Protein Coding Potential of a DNA Sequence at Computational Biosciences at Oak Ridge National Lab Note: It will be updated soon.

	Haemophilus influenzae database collection (HIDC) is a database comprised of sequences related to the Haemophilus influenzae at Justus- Liebig-University (Updated 5/1/99).
	Human Transcript Database is a curated source for information related to RNA molecules that have been sequenced. This Site is found at the Baylor College of Medicine (BCM) Search Launcher (Updated 5/1/99).

Isoelectric Point Service- a program that calculates the pI from a given amino acid sequence at EMBL, Heidelberg (Updated 5/2/99).

Java based Molecular Biologist's Workbench is a group of Java based tools that have varying levels of usefulness at EMBL-Heidelberg (Updated 4/6/99).

KEGG: Kyoto Encyclopedia of Genomes and Genes is an effort to computerize current knowledge of molecular and cellular biology in terms of the information pathways that consist of interacting molecules or genes and to provide links from the gene catalogs produced by genome sequencing projects. Genomenet, Japan. (Updated 5/2/99)

	LabOnWeb life science research engine ( membership required ) LabOnWeb is a collection of online lab protocols and life science research tools. LabOnWeb is different from other online search services in the scope of its analysis, its proprietary data and tools that it uses to enhance gene discovery and in its delivery of information. LabOnWeb protocols provide "big picture" results, giving researchers the information they need to perform more effective, efficient life science research (Updated 3/4/00).
	LALIGN - Calculates the N-Best Local Alignments Between Two Sequences at Genestream,Montpellier, France (Updated 5/1/99)
	LFASTA Local Similarity Searches Between Two Sequences Showing Local Alignments at GENESTREAM , Montpellier, France (Updated 5/2/99).

	MATCH-BOX - Simultaneous alignment of several protein sequences where each aligned position is weighted by a reliability score (Updated 8/10/00).
	MBS - ALIGNER : CLUSTALW interface for multiple sequence alignement is an interface to the famous clustalw multiple sequence alignment software. It works with standard parameters. Just type or copy your sequences (DNA or protein) at MBS - Molecular Biology Shortcuts (Updated 6/16/99)
	MBS-Enzfinder searches REBASE database for known restriction enzymes matching your query. It provides informations on: isoschizomers and related enzymes, recognition sequences, methylation, commercial availability, references at MBS - Molecular Biology Shortcuts (Updated 6/16/99).
	MBS - Quick Protein Translator this website allows the simple conversion of DNA into protein at MBS - Molecular Biology Shortcuts (Updated 6/16/99)
	MOTIF: Searching Protein and Nucleic Acid Sequence Motifs at Genomenet, Japan (Updated 5/2/99). (see PMotif)
	Multiple Sequence Alignments of Nucleic Acids and Proteins with a variety of formats including ClustalW, CAP Sequence Assembly, PIMA, etc. at the Baylor College of Medicine (BCM) Search Launcher (Updated 5/1/99)

Net-ENTREZ it is a server of protein, nucleic acid sequences, and medline at NCBI (4/6/99)

ORF and protein analysis Identify open reading frames (ORF) in DNA sequence and translate them into proteins at SUNY Geneseo Biology Department (Updated 5/2/99).

	PatternFind Server Search a protein sequence database with a pattern. (Updated 4/4/99)
	Peptide Search allows Protein identification by peptide mapping or peptide sequencing at EMBL, Heidelberg (Updated 5/1/99).
	PHILIP-Bootstrapping Analysis - Divergence Between Protein or Nucleotide Sequences at Pasteur Institute (Updated 5/2/99).
	PIR or protein information resource is a database of protein sequences at Georgetown University (Updated 6/16/99).
	pI (See Isoelectric Point Service) (Updated 5/2/99).
	PMotif determines if a protein motif is encoded by a DNA sequence or database of DNA sequences at the University of Minnesota (Updated 5/2/99). (see Motif)
	POLAND SERVER for prediction of nucleic acid's thermal stability at the Biophys Uni-D�sseldorf (Updated 5/1/99). Note: It will be moving soon.
	Primer3 picks primers for PCR reactions, considering some of the following criteria criteria: temperature, size, and GC-content at Peter O'Connell's Laboratory, University of Texas.

Alternatives	Location	Comments
Peter O'Connell's	University of Texas	release 0.1, same as above
MIT	MIT	The is the latest version of the primer picker.
MIT (old version)	MIT	One of the older versions. There is a link to the newer version of the software

Primer Selection Tool PCR primer selection program based on xprimer on the Alces WWW Server.

ProfileScan- Search a protein sequence against a
profile database at ISREC. (Updated 4/4/99)

Frame -ProfileScan Server Search a short DNA sequence against a protein profile database at ISREC.

Propsearch (at EMBL, Heidelberg)

	1) Compositional search using a sequence
	2) Compositional search using experimental Amino Acid Analysis data (Updated 5/1/99)

	PrositeScan - Search PROSITE with a sequence at ISREC. (Updated 4/4/99).
	Protein Sequence Search Tool- has a wide range of tools for analyzing the sequence of proteins found in the PDB database. The site is maintained at the Bioinformatics Genome FTP server (Updated 3/25/01).
	Psort prediction of protein sorting signals and localization sites in Amino Acid Sequences. It is is a computer program for the prediction of protein localization sites in cells. Psort Server (Updated 5/2/99).

Alternatives	Location	Comments
Psort, Okazaki	Okazaki	main
Psort, Osaka	Osaka	Alternate

PubMed - public version of medline found at the national library of medicine (NCBI) (Updated 4/6/99)

Quick Protein Translator (see MBS-Quick Protein Translator)

	Rebase, a restriction enzyme database at the rebase server (Updated 5/2/99)
	Restriction Enzyme Analysis to identify restriction mapping sites in DNA sequences at the SUNY Geneseo Biology Department (Updated 5/1/99).
	RSVP - Rapid Sequence Visualization in Postscript for Analysis of DNA Sequences at CBIL, University of Pennsylvania (Updated 5/2/99). (See the Temporary Alternative Site)

	Sequence Alerting sequence alerting system searches in several databases for news on (homologues of) a sequence and informs by email, if it has detected a new relative at EMBL-Heidelberg (Updated 5/1/99).
	Sequence Translation - Translate Gene Sequences at the University of Minnesota (Updated 5/2/99). (See DNA Sequence Translation)
	Smart - Simple Modular Architecture Research Tool: domain annotation in proteins at EMBL-Heidelberg (Updated 5/1/99)
	SRS5 (see SRS) (Updated 5/2/99)
	SRS - Sequence Retrieval System at EMBL-Heidelberg allows the user to compare the major structural and sequence databases of the world.
	SSEARCH - Universal Sequence Comparison Using the Smith-Waterman Algorithm at GENESTREAM, Montpellier, France (Updated 5/2/99).
	SwissProt is a protein sequence database that contains high-quality annotation,is non-redundant, and cross-referenced to several other databases at EMBL-Heidelberg (Updated 5/2/99). (See SwissNew)

	TESS (Transcription Element Search Software) can be used for locating and displaying transcription factor binding sites in DNA sequence at University of Pennsylvannia (Updated 5/3/99).
	TFASTA - Match a Protein Sequence Against All Six Frames of GenBank Sequences at GENESTREAM, Montpellier, France (Updated 5/2/99).
	tigr database (TDB) is a collection of curated databases containing DNA and protein sequence, gene expression, cellular role, protein family, and taxonomic data for microbes, plants and humans at the tigr institute of genomic research.

	tigr software tool collection provides a group of Java based and UNIX based programs for use in molecular biology at the tigr institute of genomic research (Updated 5/1/99).
	T_m Oligonucleotide Melting Point Determination at U. Minnesota (Updated 5/1/99).
	Translate is a tool which allows the translation of a nucleotide (DNA/RNA) sequence to a protein sequence at ExPASy, Switzerland (Updated 5/2/99).

	Vector, a searchable database at Johns Hopkins University (Updated 5/2/99) Gopher.
	Vector-ig, a searchable database of vectors that are used for molecular biology at Kyoto University, Japan (Updated 5/2/99) Gopher.
	VectorDB contains annotations and sequence information for many vectors commonly used in molecular biology by Anderson Unicom Group, Inc. (Updated 5/2/99).

	WebGene is a bioinformatics service that does ORF and protein analysis and Restriction Enzyme Analysis at Geneseo Biology Web Server (Updated 4/12/99)
	WWWSRS (See SRS) (Updated 5/2/99).

YAC data searches is a searchable database of the Yeast Artificial Chromosone at the Baylor College of Medicine (BCM) Search Laucher (Updated 5/1/99).