PASA Database sample_mydb_pasa Report

Transcripts or AssembliesCount
Total transcript seqs7359
Fli cDNAs834
partial cDNAs (ESTs)6525
Number transcripts with any alignment7243
Valid gmap alignments5650
Total Valid alignments5650
Valid FL-cDNA alignments627
Valid EST alignments5023
Number of assemblies413
Number of subclusters (genes)330
Number of fli-containing assemblies279
Number of non-fli-containing assemblies134

PASA resources:

Status Report for cDNA Assembly Annotation Comparison

Comparison # 2, Annotation Version: 2, date: 2008-06-06 20:22:27

some FL-assemblies may have been deprecated to EST status
Annotation Classification for Alignment Assemblies
FL-assembliesEST-assemblies
PASSfailPASSfail
Incorporated21083
UTR addition00
Gene extension0000
Internal gene structure rearrangement621
     -passes homology tests00
     -fails homology, passes ORF span00
Gene Merging2600
Gene Splitting00
Alt Splicing Isoform2
     -passes homology test1
1
0
     -fails homology, passes ORF span00
New Gene0023
     Alt splice of new gene0000
 
FL-assembly fails gene requirements26
Antisense106
Single-exon EST-assembly incompatible16
 
delayed incorporation due to gene merging00
delayed incorporation due to gene splitting0
 
Total413

Gene Comparison Overview

A total of 267 genes mapped to PASA assemblies
279 FL-assemblies mapped to 224 genes
Successful Incorporations by Genes
Genes supported by PASA assemblies240
Genes supported by 229 FL assemblies202
Genes supported by 68 EST assemblies only (no FL assemblies)38
Failed Incorporations by Genes
Genes failing PASA assembly incorporation79
of these, 52 genes successfully incorporate other PASA assemblies
Genes failing FL assembly incorporation46
but 24 of these genes incorporate other FL assemblies successfully.
Genes failing EST assemblies only33
The same gene may be counted in multiple categories.

Retrieve Lists of Genes Corresponding to Pass and Fail Categories.

Proposed Annotation Updates [counts as unique models, not genes]

status_idDescriptionNum Gene Model UpdatesNum Alt Splice isoforms to AddNum Novel Genes to Add
4gene-compatible fl-cdna assembly alters UTRs.000
6gene-compatible fl-cdna assembly alters protein, passed validation.000
8incompatible fl-cdna assembly alignment updates gene structure.000
9incompatible fl-cdna assembly provides alternative splicing isoform, passes validation.010
10fl-cdna assembly provides a novel gene.000
24FL-cDNA assembly stitched by EST assembly to provide alt splicing isoform.000
26FL-cDNA spans single gene and allowed to STOMP it.000
29FL-cDNA found capable of merging multiple genes200
33FL-assembly STOMPS new splice isoform000
40FL-cDNAs split single gene into multiple genes000
44FL-cDNA provides alt splicing isoform of a novel gene000
13EST assembly extends UTRs.000
14EST assembly alters protein sequence, passes validation.000
16EST assembly properly stitched into gene structure.000
17EST assembly stitched into Gene model requires alternative splicing isoform. (deprecated, see status_ids: 24,25)000
25EST assembly stitched into Gene model requires alternative splicing isoform.010
27EST-assembly stitched into a FL-alignment providing new alt splice isoform.000
31EST-stitched assembly STOMPS model lacking transcript support.000
32EST-stitched gene w/preexisting transcript support STOMPS a new alt splicing variation.000
36EST-assembly found capable of merging multiple genes.000
 Totals (some models in multiple classes)220

Summarize Gene Structure Updates to be Performed.

Comparison # 1, Annotation Version: 1, date: 2008-06-06 20:21:52

some FL-assemblies may have been deprecated to EST status
Annotation Classification for Alignment Assemblies
FL-assembliesEST-assemblies
PASSfailPASSfail
Incorporated216
UTR addition8639
Gene extension19040
Internal gene structure rearrangement620
     -passes homology tests4812
     -fails homology, passes ORF span00
Gene Merging2600
Gene Splitting00
Alt Splicing Isoform3
     -passes homology test20
3
10
     -fails homology, passes ORF span00
New Gene26025
     Alt splice of new gene8002
 
FL-assembly fails gene requirements26
Antisense105
Single-exon EST-assembly incompatible15
 
delayed incorporation due to gene merging00
delayed incorporation due to gene splitting0
 
Total413

Gene Comparison Overview

A total of 265 genes mapped to PASA assemblies
279 FL-assemblies mapped to 222 genes
Successful Incorporations by Genes
Genes supported by PASA assemblies238
Genes supported by 228 FL assemblies200
Genes supported by 67 EST assemblies only (no FL assemblies)38
Failed Incorporations by Genes
Genes failing PASA assembly incorporation77
of these, 50 genes successfully incorporate other PASA assemblies
Genes failing FL assembly incorporation45
but 23 of these genes incorporate other FL assemblies successfully.
Genes failing EST assemblies only32
The same gene may be counted in multiple categories.

Retrieve Lists of Genes Corresponding to Pass and Fail Categories.

Proposed Annotation Updates [counts as unique models, not genes]

status_idDescriptionNum Gene Model UpdatesNum Alt Splice isoforms to AddNum Novel Genes to Add
4gene-compatible fl-cdna assembly alters UTRs.8600
6gene-compatible fl-cdna assembly alters protein, passed validation.1900
8incompatible fl-cdna assembly alignment updates gene structure.4800
9incompatible fl-cdna assembly provides alternative splicing isoform, passes validation.0200
10fl-cdna assembly provides a novel gene.0026
24FL-cDNA assembly stitched by EST assembly to provide alt splicing isoform.0100
26FL-cDNA spans single gene and allowed to STOMP it.000
29FL-cDNA found capable of merging multiple genes200
33FL-assembly STOMPS new splice isoform000
40FL-cDNAs split single gene into multiple genes000
44FL-cDNA provides alt splicing isoform of a novel gene080
13EST assembly extends UTRs.3500
14EST assembly alters protein sequence, passes validation.400
16EST assembly properly stitched into gene structure.1100
17EST assembly stitched into Gene model requires alternative splicing isoform. (deprecated, see status_ids: 24,25)000
25EST assembly stitched into Gene model requires alternative splicing isoform.030
27EST-assembly stitched into a FL-alignment providing new alt splice isoform.000
31EST-stitched assembly STOMPS model lacking transcript support.000
32EST-stitched gene w/preexisting transcript support STOMPS a new alt splicing variation.000
36EST-assembly found capable of merging multiple genes.000
 Totals (some models in multiple classes)1994126

Summarize Gene Structure Updates to be Performed.

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