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Super Link:
MBS
--> Molecular
Biology Shortcuts Tools
Page.
Basically everything you need to manipulate sequences:
on-site tools and selected links
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nucleotide query Search for a nucleic acid sequence Sequence Retrieval System EMBL, not simple Vector Database Sequences of vectors used in Molecular Biology Mangone's plasmid Data-Bank Sequences, maps and info's for many commonly used plasmids Invitrogen vectors Searchable batabase of Invitrogen vectors. Includes Sequences, maps, restriction data and additional informations. Stratagene Vectors Maps and sequences of pBluescript and other Stratagene cloning vectors An effective way of finding informations, maps and sequences related to an expression/cloning vector is simply to use a meta search engine. It works very well if you know the precise name of the vector. Have a try: Bank-It
Submit a sequence to
GenBank |
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Transmembrane segments prediction Stockholm University SignalP Predicts the presence and location of signal peptide cleavage sites in amino acid sequences from different organisms PSORT Prediction of protein localization sites in cells PhosphoBase Predicts protein phosphorilation sites.CBSA, Denmark NetOglyc Predicts protein O-glycosilation sites. CBSA PREDATOR Secondary structure prediction PFAM Sanger Center. Pfam is a large collection of multiple sequence alignments and hidden Markov models covering many common protein domains |
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Blast
Search DDBJ. DNA Data Bank
of Japan C. elegans Blast Server At the Sanger Centre: Search the DNA database containing C. elegans sequence data from both the Cambridge and St. Louis Sequencing groups. Also available are the current database of C. elegans ESTs and the C. elegans protein database (wormpep).
PSI-BLAST
Position Specific Iterated BLAST.
DDBJ |
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Clustalw 1.7 : Multiple Alignements@Pasteur Clustalw EBI MBSaligner
A nice interface to crustalw
multiple sequence alignment software |
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IMAGE clone search and request EST clones IMAGE Vectors Sequences of the vectors used for the EST libraries protEST search EST databases with a protein sequence STACK Identifies EST contigs from an imput sequence The EST Assembly Machine TIGEM LabOnWeb Submit an EST/mRNA sequence to LabOnWeb. LabOnWeb elongates your sequence and provides you with a comprehensive report about your gene that includes a list of tissues in which the gene is probably expressed, guesses about gene function, mapping and more. |
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Genomic and Genetic Resources on the www At the National Human Genome Research Institute Genome sequencing Center Washington University School of Medicine MIT Center for Genome Research GOLD:
Genomes OnLine Database
Genomes Online Database, is a World
Wide Web resource for comprehensive access to information
regarding complete and ongoing genome projects around the
world. With information on 245 genomes, and over 2,000
web-links, GOLD provides the most detailed and accurate
monitoring of genome sequencing projects. |
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Primer3 Tigem version Oligo Calculator Calculate TM, %GC, picomoles/OD Web Based Primerfinder V0.06 Primerfinder is a fast and easy web based primer design program. Primerfinder can search any sequence you input for primers that meet your specifications according to several search parameters. You can specify a target primer length, annealing temp, percent GC and many other advanced search parameters. Additionally, Primerfinder can analyze candidate primers with Integrated DNA Technology's Oligo Analyzer (powered by DNASTAR) for possible hairpin and self-dimer formation. Primerfinder can also examine primers you have already created by other means with IDT's Oligo Analyzer. NetPrimer Comprehensive primer analysis, use it online or download |
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TACG
Restriction maps your DNA Sequence. A
bit complex but quite exhaustive. Many different output
formats. This is the primary TACG site. It is worthwhile to
have a look at the documentation CloneIt! An online program finding sub-cloning strategies, in-frame deletions and frameshifts using restriction enzymes and DNA polymerases ENZFINDER at MBS Searches REBASE database for known restriction enzymes matching your query. It provides informations on: isoschizomers and related enzymes, recognition sequences, methylation, commercial availability, references Translation
Machine
EBI ORF
Finder Smart graphic
output Transcriptional Element Search Software Identifies transcription factors binding sites on your DNA sequence Splice site prediction by Neural Network LBNL, US Color Protein Sequence Based on hydrophobicity, charge, and other features of your choice WWW
Promoter Scan
Predicts Promoter regions based
on scoring homologies with putative eukaryotic Pol II
promoter sequences. |
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Amos Bairock List of Links More databases exist than you ever imagined! Computational services at EMBL exPASy DNA and Protein tools Top-Class site Karolinska Institute Sequence Analysis Computer "KISAC is a bioinformatics facility, for computer aided analysis of nucleotide and protein sequences. It is used by about 40 research groups (150-200 researchers), mainly from the Karolinska Institute (KI) and the Karolinska Hospital (KS), although we have customers spread throughout Sweden" LabOnWeb.com Beta version. A simple query procedure - just submit an EST/mRNA sequence to LabOnWeb - saves you months of time at the bench. The LabOnWeb research engine automates sequence elongation and delivers a wealth of information about the full gene derived from your input sequence. Mac Software for Molecular biology Network Protein Sequence Analysis NPSA. Many tools for similarity searches, secondary structure prediction and multiple sequence alignments.Pole Bio-Informatique lyonnais Protein Data Bank PDB. The single international repository for the processing and distribution of 3-D macromolecular structure data primarily determined experimentally by X-ray crystallography and NMR. Protein Information Resource PIR List of servers useful for sequence analysis Genethon, France TIGEM Many local tools and links to remote tools. Excellent resources for EST analysis UK
MRC Human Genome Mapping Project Resource Center
Account required |
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Yeast Sequencing at the Sanger Centre The Definitive Yeast Transformation Homepage Yeast Lab Protocols from Gottschling Lab Links to Saccharomyces cerevisiae Labs Italian Yeast Cooperation Group Yale
Genome Analysis Center
This web site is devoted to a
project for large-scale analysis of gene expression, protein
localization and disruption phenotypes in Saccharomyces
cerevisiae |
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