Index of /species/data/dmel5/PASA_EST

 Name                                       Last modified       Size  Description

 Parent Directory                           23-Jun-2008 17:38      -  
 failed_gmap_alignments.gff3.gz             19-Mar-2008 03:05   999k  
 gmap_validations.gz                        19-Mar-2008 02:59  23.7M  
 output.alignment_assemblies.out.gz         19-Mar-2008 07:59   8.5M  
 output.assembly_building.out.gz            19-Mar-2008 07:43  29.0M  
 output.subclusters.out.gz                  19-Mar-2008 08:17   7.4M  
 output.tophits.btab.gz                     19-Mar-2008 02:19  19.2M  
 output.tophits.gz                          19-Mar-2008 02:18  68.2M  
 pasa_dmel.assemblies.fasta.gz              19-Mar-2008 08:25  15.7M  
 pasa_dmel.pasa_assemblies.gff3.gz          19-Mar-2008 08:44   1.5M  
 pasa_dmel.pasa_assemblies_described.txt.gz 19-Mar-2008 08:44   7.5M  
 pasa_statustable.txt.gz                    13-May-2007 21:59     1k  
 trainingSetCDS.fasta.gz                    19-Mar-2008 12:40   3.6M  
 trainingSetCandidates.fasta.gz             19-Mar-2008 12:40   2.3M  
 trainingSetCandidates.gff.gz               19-Mar-2008 12:40   1.4M  
 trainingSetCandidates.prot.blat            19-Mar-2008 15:38   6.2M  
 trainingSetCandidates.prot.duplist         19-Mar-2008 15:39   107k  
 trainingSetESTasm.fasta.gz                 19-Mar-2008 12:40   7.7M  
 validated_transcripts.gff3.gz              19-Mar-2008 08:44  19.5M  

Output of PASA (Program to Assemble Spliced Alignments)
see http://sourceforge.net/projects/pasa/ http://pasa.sourceforge.net/
The summary report is pasa_dmel.report.html from
http://server2.eugenes.org/cgi-bin/PASA/cgi-bin/status_report.cgi?db=pasa_dmel

pasa_dmel.* are main cDNA assemblies.  
Source EST drawn from NCBI dbEST/GenBank for drosmel taxon on 2008 March.
See ../fasta/dmel-est.fa for input EST data.

output.gene_structures_post_PASA_updates.*.gff3.gz is the
set of gene model corrections found from cDNA for the dmel release 5.5 
gene models.  

NOTE: ncRNA (tRNA...) and pseudogene models were removed due to limitation of this
version of PASA in handling only mRNA w/ CDS.  Thus results such as
the new models found in intergenic regions include these known ncRNAs.

-- Don Gilbert, Mar. 2008, gilbertd@indiana.edu