Useful Databases and Tools


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Literature Search

Entrez-PubMed: database of literature

Nature

Science

Current Opinion in Lipidology  (Curr. Opin. Lipidol.)

The Journal of Biological Chemistry  (J. Biol. Chem.)

Journal of Lipid Research  (J. Lipid Res.)

Biochimica et Biophysica Acta  (Biochim. Biophys. Acta)

Proceedings of the National Academy of Sciences of the United States of America   (Proc. Natl. Acad. Sci. USA)

FEBS Letters  (FEBS Lett.)

Arteriosclerosis, Thrombosis and Vascular Biology  (Arterioscler. Thromb. Vasc. Biol.)

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International Nucleotide Sequence Databases

NCBI-GenBank: National Center for Biotechnology Information

EMBL database: European Bioinformatics Institute

DDBJ: DNA databank of Japan

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Searching Database by Sequence Similarity

BLAST: at NCBI

PSI-BLAST: at NCBI

FASTA: at EBI

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Protein Sequence Databases

SWISS-PROT & TrEMBL: annotated protein database

PIR: Protein Information Resources

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Protein Sequence Alignment

ClustalW: multiple sequence alignment

T-COFFEE: multiple sequence alignment

The USC Sequence Alignment Server: pairwise alignment

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Protein Domain Families

Pfam: discover common protein domain by HMM model

PROSITE: database of protein families and domains

SMART: protein domain analysis

Protein Family Databases: introduction of protein families, including ABC superfamily

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Protein 3D Structures

PDB: database of protein 3D structures

Rasmol: viewer of protein 3D structure

SWISS-MODEL: a fully automated protein structure homology-modeling server

The PredictProtein server: a service for sequence analysis, and structure prediction

Jpred: predict protein secondary structure

PSIPRED: PSIPRED, MEMSAT and GenTHREADER

DALI: compare protein structures in 3D

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Gene Prediction and Gene Regulation Tools

GeneScan: predicting the locations and exon-intron structures of genes in genomic sequences

GLIMMER: from TIGR

Eukaryotic Promoter Database: an annotated non-redundant collection of eukaryotic POL II promoters

DBTSS: Database of Transcriptional Start Sites

Kimono: for finding regulatory elements in promoter sequences

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Other Databases and Tools

ATGpr: identifying start codon in cDNA

SignalP: predicts the presence and location of signal peptide cleavage sites in amino acid sequences

Translate Tool: translation of a nucleotide (DNA/RNA) sequence to a protein sequence

Primer3: primer design

MELTING: computing the melting temperature of nucleic acid duplex

Compute pI/Mw Tool: computation of the theoretical pI (isoelectric point) and Mw (molecular weight)

Webcutter: find restriction enzyme sites in DNA sequences

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This page is maintained by Tong. Please send your suggestions to tliu@bu.edu Thanks!
Last updated: July 9, 2002.