Databases

Repeats

Programs 

Misc.

Genotyping databases

Programs

General

Alternative splicing

Useful programs

Refs used in my PhD so far: Long version with abstracts  |  Short version

GeneOntology

VNTRfinder

Databases

• UniGene – gene orientated clusters of ESTs/mRNAs
• SWISSPROT – manually curated protein sequence database. Also see IPI, which a lot of people seem to be using nowadays – non-redundant sequences, large and from a number of sources.
• Gene Ontology (GO tools page) – hierarchical classifications of genes by biological process, cellular component and molecular function
• EnsEMBL Genome Browser
• UCSC Genome Browser
• TissueInfo – classification of EST libraries according to tissue

Genotyping databases:

• CEPH – I used to get information on repeat polymorphisms
• HapMap – over 3 million SNPs in 3 populatons
• Perlegen – about 1.5 million SNPs in 3 populations. Handy to download and heterozygosity pre-calculated.
• SeattleSNPs – genotyping of SNPs in genes related to inflammation

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Repeats

Programs

• Tandem Repeats Finder – widely used. Nucleotide repeats.
• equicktandem/etandem – from EMBOSS.
• MREPS
• RADAR – protein seqs.

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Programs

General web tools:

• BLAST
• Polydot - web tool (from EMBOSS) allowing all by all dot plots of a number of sequences.
• e-PCR - in silico PCR amplification of regions between primers

Useful downloadable programs:

• Sequence editing etc.
• JEMBOSS - EMBOSS suite of tools for bioinformatics
• BioEdit - good sequence alignment editor

• Work tools
• WS-FTP | winscp | FileZilla - good FTP clients. Winscp esp. good for SSH and secure FTP.
• CYGWIN - linux on a PC without messing up/having to partition the PC. An alternative is VMWARE but you have to pay for it L.
• wget (for windows) - retrieval of WWW pages. Can embed in a script and use to get stuff from the web. For example, to get sequences for a list of SWISSPROT accessions (from http://us.expasy.org/cgi-bin/get-sprot-fasta? where add ID after the "?")
• Bioinformaticians are messy. A useful web browser is Firefox from Mozilla. I especially love the tabbed browsing. It also has less vulnerabilities etc.

• Statistics
• R - very good open source statistical package
• STATA - I like it (prefer it to R), but you have to pay for it. 
• Databases
• MySQL - it’s free and good. Also, on Windows, if you don’t like command line tools, you should download the MySQL Administrator and MySQL Query Browser.

• Other
• Tandem repeat detection programs (see Repeats-->Programs)

Gene Ontology

• Datamining tools: GoStat | FatiGO | EASE (part of DAVID) | GOTM | GoMapper* (*use quantitative info., e.g. microarray expression data)
• AmiGO - Gene Ontology browser

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Miscellaneous

Alternative splicing:

• HASDB/ASP - Lee lab's data on alternative splicing
• VARSPLIC - sequences of alternative splice isoforms annotated in SWISSPROT

VNTRfinder:

• Detect tandem repeats
• Detect tandem repeat variation
• Predict potentially polymorphic repeats
• Web-server

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