Pseudogene information:

Finding pseudogenes is a complex task, probably more than can be done in a few
weeks. We have a selection of gene predictions noted with frameshifts, that may be
pseudogenes or assembly error.  With some human judgement, they could be
examples of psi genes in relation to in duplicate genes.

There is also, below, Pseudopipe software available that we may try to run for
Daphnia.

For the Gnomon predictions, 569 full predictions have frameshifts (of 28472),
and 504 of these have paralogs, among 224 different paralog groups.  However 383
of these have tiling expression above base line levels; 248 are strongly
expressed.  So this may be a poor marker for pseudogenes.

This is a paralog gene subset with frameshifts and no sig. expression (from
dpulex1_gnomon_annotatedgene.gff)

 Nfs Paralog    Uniprot
   6 Omcl154    Q0IG19_AEDAE/Q0IG19/Aedes aegypti/Wd-repeat protein
   6 Omcl4      TBCD_CHICK/Q5ZI87/Gallus gallus/Tubulin-specific chaperone D,Tubulin-folding cofactor D,Beta-tubulin cofactor D
   6 Omcl5      Q16TW4_AEDAE/Q16TW4/Aedes aegypti/Putative uncharacterized protein
   4 Omcl333    Q0KID9_DROME/Q0KID9/Drosophila melanogaster/CG9791-PB, isoform B
   4 Omcl779    Q0KID9_DROME/Q0KID9/Drosophila melanogaster/CG9791-PB, isoform B
   3 Omcl32     Q2M0J9_DROPS/Q2M0J9/Drosophila pseudoobscura/GA19454-PA
   3 Omcl322    Q173U6_AEDAE/Q173U6/Aedes aegypti/Transcription initiation factor TFIID subunit 6
   2 Omcl1063   Q0WLP3_ARATH/Q0WLP3/Arabidopsis thaliana/Putative uncharacterized protein
   2 Omcl114    H2B1_TIGCA/P35068/Tigriopus californicus/Histone H2B.1/H2B.2
   2 Omcl1148   HMCS1_BLAGE/P54961/Blattella germanica/Hydroxymethylglutaryl-CoA synthase 1,HMG-CoA synthase 1,3-hydroxy-3-methylglutaryl coenzyme A synthase 1
   2 Omcl137    Q28F93_XENTR/Q28F93/Xenopus tropicalis/Vacuolar protein sorting 33A,Yeast
   2 Omcl23     Q0KKB5_MAMBR/Q0KKB5/Mamestra brassicae/Heat shock protein 90
   2 Omcl2436   Q5JUZ8_HUMAN/Q5JUZ8/Homo sapiens/Programmed cell death 8,Apoptosis-inducing factor
   2 Omcl32     Q16RL8_AEDAE/Q16RL8/Aedes aegypti/BACH1, putative
   2 Omcl32     Q5DTH3_MOUSE/Q5DTH3/Mus musculus/MKIAA4210 protein
   2 Omcl333    Q9VN03_DROME/Q9VN03/Drosophila melanogaster/CG9791-PA, isoform A
   2 Omcl368    Q9NJC3_BRALA/Q9NJC3/Branchiostoma lanceolatum/Alcohol dehydrogenase class 3
   2 Omcl4      Q4SE31_TETNG/Q4SE31/Tetraodon nigroviridis/Chromosome 3 SCAF14626, whole genome shotgun sequence.
   2 Omcl4      TBCD_HUMAN/Q9BTW9,O95458,Q7L8K1,Q8IXP6,Q8NAX0,Q8WYH4,Q96E74,Q9UF82,Q9UG46,Q9Y2J3/Homo sapiens/Tubulin-specific chaperone D,Tubulin-folding cofactor D,SSD-1,Beta-tubulin cofactor D,tfcD
   2 Omcl47     Q17C76_AEDAE/Q17C76/Aedes aegypti/Focal adhesion kinase
   2 Omcl5      Q3LG56_DANRE/Q3LG56/Danio rerio/ORF2-encoded protein
   2 Omcl5      Q7T271_PAROL/Q7T271/Paralichthys olivaceus/Reverse transcriptase-like protein

Also search at wfleabase.org/cgi-bin/gbrowse/.. for "flags:Frameshifts"

.........
http://papers.gersteinlab.org/e-print/pseudopipe/
with software at
http://www.pseudogene.org/DOWNLOADS/pipeline_codes/

"These high-confidence pseudogenes are then classified as (1) retro- 
transposed pseudogenes, (2) duplicated pseudogenes and (3) pseudogeneic 
fragments. Retrotransposed pseudogenes lack introns, have small flanking 
direct repeats and a 30 polyadenine tail."