New Gene Recognoition Software (Procrustes 4.0)

[Pavel Pevzner]

Announcement: New version of Procrustes gene recognition software. 
 
The new version 4.01 beta of Procrustes is available as a WWW server:
 
          http://www-hto.usc.edu/software/procrustes/
 
Procrustes 4.0 is geared towards computational support of experimental
gene identification and annotation-quality gene predictions. 

The new distinctive features of Procrustes 4.01 are:

- identification of  genes and exons for which the predictions
  are guaranteed to be correct (Las Vegas gene predictions) 
- error-tolerant gene recognition 
- construction of  primer cover for PCR-based gene identification 
  in large-scale sequencing projects (GenePrimer software)
- highly specific recognition of exons for selection of 
  probes and PCR primers to cDNA (CASSANDRA software)
- recognition of incomplete genes in unfinished cosmid-size genomic 
  sequences via local spliced alignment 
- new graphical outputs for multiple gene predictions and experimental 
  gene identification
- assignment of  confidence levels to gene predictions
- multiple gene predictions via suboptimal spliced alignment
- gene recognition based on similar domains rather than entire proteins
- gene recognition in different species.


PROCRUSTES is now available in  commmand line version
for incorporation in  DNA sequence analysis  pipelines. 

The previous version of Procrustes is described in 

          Gelfand, M.S., Mironov, A.A.,Pevzner, P.A. 
          "Gene recognition via spliced sequence alignment", 
          Proc. Natl. Acad. Sci. USA (1996), 93, 9061-9066

and is protected by 

U.S. patent application "Combinatorial Gene Recognition" 60/035,720.