Nucleic Acid/Protein Analysis

- Sequence Homology

• FASTA: EBI | DDBJ |
• BLAST: EBI | Genome Net | NCBI | DDBJ
• Smith & Waterman: DISC (mail) | EBI | DDBJ
• Multi: GenQuest |

- Nucleic Acid

• Gene Prediction:
  • FramePlot - protein-coding region prediction in bacterial DNA with a high G+C-content.
  • GeneHacker
  • GeneMark
  • GENSCAN: MIT | dkfz | Pasteur
  • GRAIL
• Java Ribosome - DNA -> Protein translation [Java]
• KiloAce - fragment size estimation tool for agarose electrophoresis
• Oligo feature
  • Oligo Calculator - calculate Tm, M.W., GC%, etc. [Java]
  • Tm Determination - oligonucleotide melting temperature
• Open Reading Frame Search
  • ORF Finder
  • WebGene ORF and protein analysis
• PROSCAN - Predicts Promoter regions based on scoring homologies with putative eukaryotic Pol II promoter sequences
• PCR
  • Primer design: Primer3 | GeneFisher2 | PrimerQuest
• RNAi & siRNA
  • Design: siDirect | SiRNA at Whitehead | siRNA selector | siSearch | siRNA Elite | BLOCK-iT^TM RNAi Designer | RNAi Design
• Sequence manipulation
  • ReadSeq - an interface for a sequence format convertor
  • Reverse, Complement or Reverse and Complement [Java]
• Restriction analysis
  • WWWtacg - reports restriction data as table, linear map, pseudo-gel pattern, and etc.
  • Webcutter - an on-line tool for restriction mapping
  • WebGene Restriction Enzyme Analysis
• SIGSCAN - Find and list homologies of published signal sequences with the input DNA sequence
• tRNAscan - tRNA detection tool

- Protein

• Amino Acid Sequence Motif:
  • BLOCKS
  • CDD - Conserved Domain Database
  • MOTIF (Genome Net)
  • Pfam
  • PROSITE (EBI)
  • SMART
• Secondary Structure:
  • BCM protein secondary structure
  • NNPREDICT
  • PredictProtein - PHD, TOPITS, MaxHom, EvalSec
• BioMagResBank - a database of NMR-derived protein structures
• pI/Mw - a tool which allows the theoretical pI and Mol.wt.
• Protein Kinase Resource (PKR) - a web accessible compendium on protein kinases [Mirror]
• PSORT
• SignalP - predicts the presence and location of signal peptide cleavage sites
• SWISS-MODEL - an automated knowledge-based protein modelling server (3D-structure prediction)

- Alignment

• ClustalW: GenomeNet | DDBJ
• DiAlign - no gap penalties

- Phylogeny

• BOXSHADE - creating pretty output of mutiple aligned protein/DNA data. ClustalW and MSF (GCG) formats are available.

- Multi-purpose

• BCM Search Launcher
  
  • Gene Finder - Splice sites, Protein coding exons and Gene model construction
  • Prorein secondary structure prediction - SSP, Segment-oriented prediction; NNSSP, Nearest-neighbor prediction
• ExPASy tools
• GenQuest
• JaMBW - Java based Molecular Biologist's Workbench
  
• NCSA BIOLOGY WORKBENCH
• Prot-Web