EMBOSS: C2 Applications

Required by Sanger Centre

The following applications are specified in the original EMBOSS grant application. They replace obsolete EGCG applications in routine use at the Sanger Centre.
  1. EST clustering (findoverlap, checkoverlap, clusteroverlap, alignoverlap) originally writen for CpG island clustering, now replaced by other utilities and by
  2. Rapid database searching with sequence patterns (stssearch)
  3. Rapid database searching for sequence overlaps (equickindex, equicksearch, quickmatch)
  4. Repeat identification (etandem, equicktandem, einverted)
  5. Nucleotide pattern analysis (cpgspans, cpgplot)
  6. Codon usage analysis for small genomes (codfish)
  7. Gene identification tools (est_genome)
  8. Rapid identification of sequence patterns in large sequence sets (wordup, wordcount, chaos, polydot)
  9. Protein motif identification and domain analysis (pepcoil, antigenic, sigcleave)
  10. Presentation tools for publication (prettyplot)

First Applications

In addition to many new applications, some useful utilities have been written to test the library code and will be of general use.

See the EMBOSS Applications web pages for a complete list of applications in the current release.

See also the EMBOSS Applications web pages and the New Applications topic.