Index of /EvidentialGene/arthropods/daphnia/daphnia_magna/Genes/modelled_on_genome
 Name Last modified Size
![[DIR]](/icons/back.gif) Parent Directory 22-Sep-2016 14:57 -
![[ ]](/icons/compressed.gif) daphmagna_201104m8.aa.gz 10-Apr-2011 13:54 6.9M
daphmagna_201104m8.alttransnew.aa.gz 12-Apr-2011 15:49 1.3M
![[TXT]](/icons/text.gif) daphmagna_201104m8.annot.readme.txt 30-Oct-2011 14:03 3k
daphmagna_201104m8.annotable.txt.gz 10-Apr-2011 15:36 1.4M
daphmagna_201104m8.cds.gz 10-Apr-2011 14:00 8.7M
daphmagna_201104m8.gff.gz 10-Apr-2011 15:46 17.5M
daphmagna_201104m8.pasaupdate.gff.gz 12-Apr-2011 15:21 12.4M
daphmagna_201104m8.pasaupdate.gtf.gz 12-Apr-2011 15:33 4.2M
daphmagna_201104m8.summary.txt 12-Apr-2011 23:10 5k
daphmagna_201104m8.tr.gz 10-Apr-2011 13:54 18.1M
Gene files:
1505610 Apr 10 15:36 daphmagna_201104m8.annotable.txt.gz gene annotation table
18297922 Apr 10 15:46 daphmagna_201104m8.gff.gz gene feature locations
7183738 Apr 10 13:54 daphmagna_201104m8.aa.gz fasta protein
9070872 Apr 10 14:00 daphmagna_201104m8.cds.gz fasta coding na
18979950 Apr 10 13:54 daphmagna_201104m8.tr.gz fasta transcript
12978345 Apr 12 15:21 daphmagna_201104m8.pasaupdate.gff.gz gene feature updates
12978345 Apr 12 15:21 daphmagna_201104m8.pasaupdate.gtf.gz above file in GTF format
1397110 Apr 12 15:49 daphmagna_201104m8.alttransnew.aa.gz fasta alt-proteins not same as primary
daphmagna_201104m8.pasaupdate includes PASA est/rna-seq validated gene model corrections,
and addition of alternate transcripts, plus 201 additional good genes missed before.
Gene Evidence Summary for daphnia_magna, 2011mar
Evid. Nevd Statistic 2011m8 2010ep24 2011m8update
------ ------ ------------- ------ ------ ------
EST 26Mb BaseOverlap 0.822 0.722 0.848
Pro 27Mb BaseOverlap 0.819 0.727 0.823
RNA 32Mb BaseOverlap 0.684 0.551 0.714
Intron 88981 SplicesHit 0.937 0.861 0.937
T'poson 844Kb BaseOverlap 0.634 0.486 0.635
Specif 54Mb BaseOverlap 0.398 0.418 0.407
ESTgene 12009 Perfect 6495 1516 8038
ESTgene 12009 Sensitv. 0.841 0.652 0.890
ESTgene 12009 Specifc. 0.720 0.626 0.751
Progene 19252 Perfect 8859 6722 9235
Progene 19252 Sensitv. 0.745 0.690 0.749
Progene 19252 Specifc. 0.719 0.700 0.723
Homolog -- homolog.Nfound 21028 17856 --
Homolog -- homolog.bits/aa 0.995 0.989 --
Paralog -- paralog.Nfound 19228 14475 --
Paralog -- paralog.bits/aa 0.926 0.786 --
Genome -- Coding Mb 31mb 27mb 31mb
Genome -- Exon Mbase 53mb 41mb 55mb
Genome -- Gene count 34614 23478 34815
Genome -- alternate tr -- -- 12641 on 5883 genes
------------------------------------------------------------
Predictions: 2011m8=bestgenes_of8.an8b.gff, April 2011
ep24 = dmag_ep24augmap2an2.gff, prerelease3 on 2 May 2010
2011m8pp= daphmagna_201104m8.pasaplus.gff, April 2011
..............................................
Gene Models Summary for daphnia_magna, 2011mar
------------------------------------------------------------
Count of genes from 2011m8 = genes/bestgenes_of7.an8b.gff
34614 Genes (version: 2011m8, mix8b)
Evidence support:
33897 have evidence (homology, EST or RNAseq)
26870 have Protein homology
12256 have orthologs (>=33%)
10185 have in-paralogs (>=33%)
28619 have Expression (EST or RNAseq)
15297 have EST (>=33%)
15928 have RNAseq (>=33%)
22753 have >= 95% evidence coverage
28126 have >= 66% evidence coverage
31608 have >= 33% evidence coverage
Quality of models:
18176 are full protein genes (complete and protein coding)
6388 are partial protein genes (for missing start, internal stops)
10050 are noncoding genes (for pCDS <= 0.33 or lenCDS < 120)
374 have transposon match >=33%
... 2011m8update ...
Count of genes from genes/daphmagna_201104m8.pasaplus.gff.gz
34815 Genes (version: daphmagna_201104m8update; 201 genes added)
12641 Alternate Transcripts on 5883 genes
------------------------------------------------------------
D.magna potential missed genes from un-mapped rna-seq reads:
transcript first assemblies: n=38653, size= 5 megabases
transcript all assemblies: n=42549, size= 6 megabases
Summary comparison of 3 arthropod gene and transcript evidence
Daphia magna, Daphnia pulex, Pea aphid
daphnia_magna, 2011mar daphnia_pulex, 2010 pea_aphid, 2011mar
Evid. Nevd Dmagm8 Evid. Nevd Dplx2 Evid. Nevd Aphid2
------ ------ ------ ------ ------ ------ ------ ------ ------
EST 26mb 0.822 EST 12mb 0.884 EST 36mb 0.813
Pro 27mb 0.819 Pro 21mb 0.831 Pro 27mb 0.786
RNA 32mb 0.684 RNA 42mb 0.677 RNA 55mb 0.428
Intron 89k 0.937 Intron 68k 0.963 Intron 127k 0.690
TAR 36Mb 0.791
Coding span 31 mb Coding span 48 mb Coding span 42 mb
Exon span 53 mb Exon span 71 mb Exon span 74 mb
Genome size 131 mb Genome size 227 mb Genome size 541 mb
Gene count 34614 Gene count 47712 Gene count 32967
--------------------------------------------------------------------------
Nevd for EST, Pro, RNA is total span of non-overlapping reads or alignments,
but count for good, unique Intron sites from spliced reads.
Best protein homology for Daphnia magna is slightly lower than Daphnia pulex:
N_match Align Bitscore
d.pulex x tribolium: 10739 392 332 d.pulex genes2010
d.magna x tribolium: 10713 376 319 d.magna 2011m8update
d.magna x tribolium: 10526 369 309 d.magna 2010 alpha
d.pulex x human: 14356 378 301 d.pulex genes2010
d.magna x human: 14335 368 290 d.magna 2011m8update
#............................................................
produced using EvidentialGene annotation software from
http://arthropods.eugenes.org/EvidentialGene/
by Don Gilbert
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