cDNA/EST assembly for Acyrthosiphon_pisum
using PASA (Program to Assemble Spliced Alignments)
See also Assembly reports and annotation maps for pea aphid

 Name                                           Last modified       Size  Description

 Parent Directory                               18-Jul-2008 15:12      -  
 failed_gmap_alignments.gff3.gz                 04-Jun-2008 16:36  1008k  
 gmap_validations.gz                            04-Jun-2008 16:35   7.8M  
 output.alignment_assemblies.out.gz             04-Jun-2008 17:04   2.9M  
 output.alt_internal_exon_finding.out.gz        07-Jun-2008 16:22     1k  
 output.alt_splice_FL_FL_compare.gz             07-Jun-2008 16:29   810k  
 output.alt_splice_label_combinations.dat.gz    07-Jun-2008 16:29    73k  
 output.alt_splicing_analysis.gz                07-Jun-2008 16:13   953k  
 output.assembly_building.out.gz                04-Jun-2008 16:59   8.2M  
 output.indiv_splice_labels_and_coords.dat.gz   07-Jun-2008 16:29   931k  
 output.subclusters.out.gz                      07-Jun-2008 15:09   2.2M  
 output.tophits.btab.gz                         04-Jun-2008 16:29   7.6M  
 output.tophits.gz                              04-Jun-2008 16:28  22.9M  
 pasa-info.txt                                  07-Jun-2008 13:22     5k  
 pasa.terminal_exons.gff3.gz                    13-Jun-2008 21:47   370k  
 pasa_acyr.alt_splicing_events_described.txt.gz 07-Jun-2008 16:29    46k  
 pasa_acyr.assemblies.fasta.gz                  04-Jun-2008 17:11   6.4M  
 pasa_acyr.correlated_splicing_features.tab.gz  07-Jun-2008 16:29    29k  
 pasa_acyr.pasa_assemblies.gff3.gz              04-Jun-2008 17:54   1.0M  
 pasa_acyr.pasa_assemblies_described.txt.gz     04-Jun-2008 17:20   2.4M  
 pasa_acyr.status.html                          11-Aug-2008 13:34     2k  
 pasa_acyr.train33SetCDS.fasta.gz               07-Jun-2008 13:43   2.2M  
 pasa_acyr.train33SetCandidates.fasta.gz        07-Jun-2008 13:43   1.5M  
 pasa_acyr.train33SetCandidates.gff.gz          15-Jun-2008 19:23   1.4M  
 pasa_acyr.train33SetESTasm.fasta.gz            07-Jun-2008 13:43   5.6M  
 pasa_acyr.validated_transcripts.gff.gz         15-Jun-2008 19:18   5.5M  
 train33SetCDS.fasta.gz                         07-Jun-2008 13:43   2.2M  
 train33SetCandidates.fasta.gz                  07-Jun-2008 13:43   1.5M  
 train33SetCandidates.gff.gz                    07-Jun-2008 13:43   1.6M  
 train33SetESTasm.fasta.gz                      07-Jun-2008 13:43   5.6M  
 trainingSetCDS.fasta.gz                        04-Jun-2008 18:21   1.5M  
 trainingSetCandidates.fasta.gz                 04-Jun-2008 18:21   996k  
 trainingSetCandidates.gff.gz                   04-Jun-2008 18:21   820k  
 trainingSetCandidates.prot.blat                04-Jun-2008 20:19   1.5M  
 trainingSetCandidates.prot.duplist             04-Jun-2008 20:21    38k  
 trainingSetESTasm.fasta.gz                     04-Jun-2008 18:21   2.9M  
 validated_transcripts.gff3.gz                  04-Jun-2008 17:20   7.1M  

Output of PASA (Program to Assemble Spliced Alignments)
for Acyrthosiphon_pisum EST data (from NCBI GenBank, 08 june)

see http://sourceforge.net/projects/pasa/ http://pasa.sourceforge.net/
The summary report is pasa_acyr.report.html from
http://server2.eugenes.org/cgi-bin/PASA/cgi-bin/status_report.cgi?db=pasa_acyr

pasa_acyr.* are main cDNA assemblies.  See ../fasta/acyr-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 NCBI Gnomon (Acyr 1.0)
gene set.

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