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Molecular Biology Database Searches


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Literature Citation Search Programs

o The Entrez Browser is a way to search a molecular biology subset of Medline, as well as protein and nucleotide databases. (updated every 2 months) (NCBI)
o Sequence Retrieval System (SRS) Network Browser for Databanks in Molecular Biology. Searches 35 or more databases. (EBI)
o Text-based search of Genbank, SWISS-PROT, and PIR. (updated daily)(NCBI)
o DBGET Integrated Database Retrieval System searches GeneBank, EMBL, SWISS-PROT, PIR, PRF, LITDB, PDB, PDB STR, EDP, PROSITE, LIGAND, PMD, AA-Index, OMIM. (GenomeNet)
o OWL-protein sequence search is a non-redundant protein sequence database produced from the following source databases: SWISSPROT, PIR(1-3), Genebank translations, and NRL-3D. (Johns Hopkins)

Sequence Homology Search Programs

o BLAST:Basic Local Alignment Search Tool is for searching for homology between your nucleotide of protein query sequence and sequences in PDB, GenBank(R) and translations and updates, EMBL and updates, SWISS-PROT, and PIR(R). (NCBI)
o Sequence Similarity Searches includes choice of: FASTA, BLITZ, PROSITE, BLAST, and BCM Search Methods (EBI).
o Clustalw allows you to perform multiple sequence homology searches via a web interface.
o MOTIF: Searching Protein Sequences Motives against PROSITE (by Univ of Geneva) Dictionary or MotivDict Dictionary (by ICR, Kyoto Univ.)(GenomeNet)

Protein Structure Prediction/Modeling Programs

o PredictProtein predicts secondary structure/accessibility based on protein sequence information.(EMBL)
o PROPSEARCH uses the amino acid composition instead of typical alignment methods to determine the putative protein family.(EMBL)
o DALI provides a comparison of protein structures in 3D. (EMBL)
o K2D predicts protein secondary structure from CD spectra.(FTP site only) (EMBL)

PCR Primer Analysis

o Net Primer is a java applet which you can download and analyse your primers quickly.
o Primer 3 is the oldest primer analysis tool in an updated version. Created by the Whitehead Institute, its a great tool to use. Now with a cgi version.
o PrimerDesign is a dos tool you can download. Look for a new version soon (2.1).

On-line Submissions to Databases

o BankIt allows you to use the World Wide Web (WWW) to submit sequences to GenBank. (NCBI)
o The EBI Sequence Data Submission System walks you through sequence subimssions through a series of forms which divide this highly complex task into smaller, more managable tasks. (EBI)

UMKC Molecular Biology Database Index

o The UMKC Molecular Biology Database Index is a growing list of nucleotide, protein and genomic databases located throughout the world. Each database is provided with a description, and a hot-link to a site from where it can be searched.

Summary of Primary Databases

Soon these links will be directed directly to the UMKC Index of Molecular Biology Databases
DNA Databases
oEMBL (European Molecular Biology Laboratory)
oDDBJ (DNA Database of Japan)

Protein Databases
oProtein Data Base

DNA Tagged Sites, Mapping data and Protein Pattern Databases
odbSTS (Database of Sequence Tagged Sites)
o dbEST (Database of Expressed Sequence Tags)

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