BIO INFORMATICS
- Peptide analysis tools
- DNA -> protein
- Similarity search
- Ultrafast rigorous searches: bioaccelerato
- Pattern and profile searches
- Gene finders and other sequence analysis programs
- Databases
- Motif Search
- Primary structure analysis
- Secondary Structure Prediction
- Tertiary structure
- Transmembrane regions detection
- Sequence alignment
- Modelling Software
- AACompIdent
- AACompSim
- MultiIdent
- PeptIdent
- TagIdent
- FindMod
- PeptideMass
- Compute pI/Mw
- ProteinProspector
- PROWL
- PeptideSearch
- MOWSE
- Mascot
- CombSearch
Similarity searches: BLAST and WU-BLAST
- BLAST at NCBI
- WU-BLAST at EMBnet-CH
- BLAST 2.0 at EMBnet-CH
- WU-BLAST at Bork's group in EMBL (Heidelberg)
- WU-BLAST and BLAST at the EBI (Hinxton)
- BLAST at PBIL (Lyon)
Ultrafast rigorous searches: bioaccelerato
- ScanProsite
- PROSITE
- ProfileScan
- Frame-ProfileScan
- Washington University Pfam HMM
- Sanger Centre Pfam
- Bipartite NLS Locator
- FPAT
- PRATT
- PPSEARCH
- PROSITE scan at PBIL
Gene finders and other sequence analysis programs
- Glimmer
- GENSCAN
- GeneSplicer
- GlimmerHMM
- TigrScan
- TransTerm
- MUMmer
- Bambus
- Genie
- GRAIL
- GeneID
- GeneMark
- NetPlantGene
- Promoter Prediction by Neural Network
- SplicePredictor
- Jigsaw
- TESS
- Genotator
- WebGene (GenView, ORFGene, SpliceView)
- The Staden Package
- PatternHunter
- GeneHacker
- Geneid
- GeneSeqer
- GenBank
- The NCBI WWW Entrez PubMed Browser
- GeneCards
- The EpoDB (Erythropoiesis Database)
- PDD, the NIMH-NCI Protein-Disease Database
- SRS
- Homstrad
- PROSITE Search Form
- Motifs in protein databases
- Screening pattern or alignment against PROTEIN databank
- COGnitor
- HMMER Sean Eddy
- emotif
- FunSiteP
- SMART
- SAM
- here
- ProtParam
- MW, pI, Titration curve
- ProtScale
- SAPS
- SAPS at EBI
- PSORT
- SignalP
- ChloroP
- NetOGlyc
- NetPicoRNA
- Coils
- Coils at PBIL
- Paircoil
- Multicoil
- HLA_Bind
- PEST
- Drawhca
- Protein Colourer
- Colorseq
- HelixWheel
- RandSeq
Secondary Structure Prediction
- AGADIR
- BCM PSSP
- DSC
- GOR at PBIL
- GOR at SBDS
- GOR II (Gibrat et al, 1987)
- GOR IV (Garnier et al, 1996)
- HNN
- Jpred
- nnPredict
- PredictProtein
- PREDATOR
- PSA
- PSIpred
- SOPM (Geourjon et Del?age, 1994)
- SOPMA (Geourjon et Del?age, 1995)
- SSPRED
- THREADER2
- Predict Protein
- RAPTOR, Prospect Pro
- NNPREDICT
- PSA Protein Structure Prediction Server
- RNA secondary structure prediction
- SoWhat
- PREDATOR
- environ
- confmat
- melting
Transmembrane regions detection
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