Sequence Analysis

1. Nucleotide analysis tools
   • Blast your sequence against nr in NCBI

   • Blast your sequence against all seqs in TIGR-CMR

   • Multiple sequence alignment: ClustalW in BioEdit and TreeView

   • Dot Plot: Dot or matrix plots provide an easy and powerful means of sequence analysis, useful for searching out regions of similarity in two sequences and repeats within a single sequence.

   • Having Problems in heterologous gene expression? Do A Codon Usage Analysis.

2. Protein analysis tools
   • Blast your sequence against nr in NCBI

   • Blast your sequence against all seqs in TIGR-CMR

   • Blast your sequence against all seqs in SWISS-PROT

   • Multiple sequence alignment: ClustalW in BioEdit and TreeView

   • PSORT: Predict the Sublocalization of your protein

   • Does you protein have a Signal Peptide? Try SignalP for the presence and location of signal peptide cleavage sites in amino acid sequences.

   • Protein Motif and Secondary Structure prediction tools
     • PROSITE: which consists of biologically significant sites, can help to reliably identify to which known protein family (if any) a new sequence belongs.

     • Pfam: a large collection of multiple sequence alignments and hidden Markov models covering many common protein families.

     • SCOP: Structural classification of proteins.

3. RNA Secondary Structure Prediction

4. Phylogenetic Analysis
   • PHYLIP

   • Multiple sequence alignment: ClustalW in BioEdit and TreeView