Summer Schools
2006 Toolbox

Remember: This is not an exhaustive list but any tool included here must be free to use, student friendly, stable and well supported

Remember: Your tutor will provide specific instruction and demonstration in the correct use, advantages and limitations of each tool throughout the teaching session.

Remember: Speed of response and total users may vary with local time around the world. It may pay for you to favour resources in one continent or another depending on your location and the time of day!

Remember: Links may age or go down so be prepared to search out replacements.

Remember: If two tools claim to do the same job but use different approaches then you will benefit from critically comparing the output of each for both concurrence and disagreement

Using the literature

• Right now : PubMed (US)
• Continuously : PubCrawler (Europe)

Collecting Sequences and other information

• SRS (Europe 1, Europe 2)
• Entrez (US)
• ExPASY (Europe)

Exploiting Sequences

• Find the Open Reading Frame and Translate (US 1, US 2)
• Designing PCR primers (US)
• Restriction enzyme digestion of DNA (US)
• Knockdowns: Design interfering RNA (US?)

Comparing Sequences

• BLAST2 (Europe) (US: includes f and y BLAST options)
• ClustalW; for multiple sequence alignment (Europe)
• Multalin; for multiple sequence alignment (Europe)
• Manual for multiple sequence alignment editor(Europe)
• Boxshade; printer and word processor friendly output (Europe)
• Phylogeny resources (US)

Analysing Sequences

• SMART: Finding domains (Europe)
• Blocks: no gaps, manually curated (US) (Europe)
• FingerPrints: with gaps, manually curated (Europe)
• Pfam: HMM, manually curated (US), (Europe 1, Europe 2)
• TIGRFams: HMM, manually curated (US)
• Prodom: automatically generated familes (Europe)
• Interpro: integrated system (Europe)
• Phosphobase: predicting phosphorylation sites (Europe)
• Scansite: kinase site & binding domain profiles (US)
• Mass and isoelectric point (Europe)

Analysing Structure

• JPRED: secondary structure prediction (Europe)
• @TOME; Simultaneous multiple modeling (Europe)
• drawhca: Identify domains through hydrophobic cluster analysis (Europe)
• PDB: existing structure models (US) (Europe)
• Swissmodel: structural model prediction (Europe)
• CE: Structure superimposition (US)
• FUGUE: find distant homologues by sequence-structure comparison (Europe)
• Transmembrane domains & topology
• Sosui (Japan)
• Kyte-Doolittle (US)

Analysing Genomic sequences

• ENSEMBL: gene ID, automated compilation (Europe)
• NHGRI: genome resources (US)
• MapViewer: gene ID, wide scope (US)
• CONFAC: Promotor hunting (US)
• TFBIND: finding transcription factor binding sites (Japan)
• PROMO: finding transcription factor binding sites (Europe)
• GeneNetWorks: gene expression regulation (Europe)
• MatInspector: finding transcription factor binding sites (Europe)
• Target Explorer: predicting regulated genes for a given transcription factor (US)
• A promotor tool box: general promotor tools (Europe)

Analysing Disease

• OMIM: Diseases and inheritance (US)
• Genecards: Diseases and genes (Europe)

Additional Resources

• Amino acids: structures and codes (Europe) (US1, US2)
• LITBIO: A large compedium of useful bioinformatic resources (Europe)
• Developmental biology on line, includes glossary (US)
• Life Science Glossary (US)

Modeling the embryo

• Virtual Embryo (Ascidian Network for In Situ Expression and Embryological Data) (Link)

A
Geraint Thomas,
Department of Physiology,
UCL
Production