Bioinformatics Links (originally Links for Workshop exercises):

Spiroplasma kunkelii sequences
Display of multiple alignments via Boxshade
BLAST page
Rockefeller University's compact index Links to most available services)
NCBI tools page
FASTA3 at EBI
Advanced BLAST
Predict Protein
Primer3 web service
RNAfold
Reverse complement: Sequence Manipulation Suite
HHPRED uses PSI-BLAST to predict structure
Compass also uses PSI-BLAST to predict structure
FFAS03 does the same
Cytoscape Network visalization software
eecm energy correlation matrix estimation (Kael Fischer)
UChip Utah version of e-predict

Links to databases

Database issue of Nucl. Acids Res.
Primary databases

GenBank (nucleotide sequence)

Nucleotide
EST (expressed sequence tags)
GSS (genome survey sequences)
STS (sequence tagged sites)
RefSeq (reference sequences--standards for comparisons)

EMBL(nucleotide sequence)
DDBJ(nucleotide sequence)
SwissProt(protein sequence)
PIR(protein sequence)
PDB(3-D structures)
Enzyme nomenclature

small RNA database at Delaware

Meta-database services

NCBI

Assistance

Databases

Nucleotides (GenBank)
Proteins (Compilation)
Structure (3-dimensional, MMDB)
Genomes (maps, stats, etc.)
Medical literature (PubMed)
Taxonomy

Database listing
SRS, the search service

Secondary databases

Protein motifs and domains

BLOCKS (conserved protein regions)
Prosite (protein motifs)
PRINTS (protein motifs) alternate
ProDom (arrangements of protein domains)

ProDom of completed microbial genomes

InterPro tertiary database (Pfam, PRINTS, PROSITE, ProDom)
AllAll (database self comparison of protein sequences)

Protein function

PFam (HMM domain identifications)
Clusters of Orthologous Groups (COG)

Phylogeny, Taxonomy, Evolution

PopSet (sequences from populations)
Ribosomal RNA

US (RDP)
Europe

Protein structure

MMDB (Molecular Modeling DataBase)
Fold recognition

SCOP (MRC Cambridge)
CATH (University College, London)
FSSP (EBI, Cambridge)
3 Dee (Dundee)
HOMSTRAD (Biochemistry, Cambridge)
VAST (NCBI, USA)

SMART (Simple Modular Architecture Research Tool) (Alternate)

Links to server resources on the web

Meta-servers

Tools at NCBI (tutorials)
EBI (searches, etc.)
BCM Search Launcher
ExPasy (Protein)
Sequence Manipulation Suite
Meta-Predict Protein (alternate)
GeneQuiz (predicting protein function)
MultAlign (for protein multiple sequence alignments) (Alternate)

Specific servers

FASTA searches (GWFASTA)
Proteins

Protein motifs (e-Motif) (alternate)
Conserved Domain Database (CDD)
HMMER and NAIL (A HMM search for protein motifs and its display)
LOOPP
CPHmodels
SDSC1
Swiss-Model

RNA structure

RNAfold
Zuker's Mfold

Repeat identification and handling in primary sequences

REPRO for proteins, slow, but sensitive
Repeats also for proteins, faster, but less sensitive
Reputer for DNA.

Primer and probe design
- MFEPrimer Improved specificity over other PCR design algorithms. Search against limited host organism set.
- Primer Tools from NISTwill evaluate hairpins and dimers on multiple primers.
- DNAssist for PC's
- Oligonucleotide design MAD_DPD (download) (Article) This software allows design of a minimal number of degenerate oligonucleotides to cover a somewhat conserved region in highly diverse set of molecules. It uses a simulated annealing type strategy
- Batch Primer3 is a server that will pick multiplex primers from a given
  sequence
Sequence alignment
- PRANK The only application I know that positions gaps with some phylogenetic sense behind the positioning. (available from Nick Goldman's site at ebi.ac.uk)
Phylogenetic reconstruction
- DIVEIN (Mullins)
- Felsenstein's list
- PAUP* (Swofford)
- MacClade (Maddisons)
- Mesquite--Modules for assembling phylogenetic programs
- Modeltest (Posada)--Which models for molecular evolution best explain your data?
- RDP3 (Martin) --an integrated suite of methods to detect recombination events in sequences
- Cophylogeny (Charleston) --TreeMap and related items
Structure display and comparison
- Molecular graphics software list
- Cn3D (3-D viewer for browsers)
- SchiSM (Chime-compatible web pages)
Bioinformatics courses, programs and tutorials
- NCBI Education
- Listing of courses and programs
- Listing of Tutorials
  - Sequence analysis tutorial
  - Protein structure prediction
Molecular genetics webtext
Last updated: 7 July 2011