euGenes/Arthropods About EvidentialGene BLAST Gene Search Maps Data DroSpeGe

Index of /arthropods/data

      Name                    Last modified       Size  Description

[DIR] Parent Directory 06-Dec-2012 12:53 - [DIR] aphid/ 06-Sep-2011 14:56 - [TXT] arp2sources.txt 06-Sep-2011 14:48 2k [DIR] blackfly/ 06-Sep-2011 15:19 - [DIR] daphnia/ 06-Sep-2011 15:01 - [DIR] ixodes/ 01-Dec-2009 19:02 - [DIR] nasonia/ 04-Feb-2010 14:57 - [DIR] proteomes/ 06-Sep-2011 14:43 -


euGenes/Arthropods Source data notes, version ARP2 2009 December
METHODS: Arthropod OrthoMCL gene clustering

Species          	N_Tr	N_Gene	Source

Aedes aegyptii   	17,402	16,004	Vectorbase AaegL1.2 July, 2009
Anopheles gambiae	14,103	12,607	Vectorbase AgamP3.5 July 2009
Culex pipiens   	18,883	18,779	Vectorbase/Broad CpipJ1.2 June 2008
Drosophila melanogaster	18,476	14,063	FlyBase release 5.22, Sep 2009
Drosophila pseudo.	19,259	17,677	NCBI Gnomon CAF1 May 2006
Drosophila mojav.	17,950	16,469	NCBI Gnomon CAF1 May 2006
Bombyx mori     	14,623	14,517	SilkDB.org Glean_genes release 2, Aug 2009
Tribolium castaneum	16,645	16,437	Beetlebase OGS release 3, 2009
Apis mellifera  	17,182	14,096	NCBI Gnomon
Nasonia vitripennis	27,287	26,141	NCBI Gnomon Dec 2007
Pediculus humanus	10,775	10,759	Vectorbase PhumU1.2 Mar 2009
Acyrthosiphon pisum	37,783	34,409	NCBI Gnomon June 2008
Daphnia pulex   	37,329	30,770	NCBI Gnomon/wFleaBase May 2007
Ixodes scapularis	20,486	20,311	Vectorbase IscaW1.1 Nov 2008


N_Tr count includes all alternate transcripts available.
N_Gene count is final analyzed count of one-transcript per gene per species.
Proteins are from protein coding gene models, 
including, where provided, partial and frameshifted models.  Alternate
transcripts where removed after blast matching, to determine best-matching
transcript.  6000 alt-tr in drosmel, less than 1000 in others.

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Data accessed Fall 2009
Source URLs
  NCBI Gnomon: ftp://ftp.ncbi.nih.gov/genomes/...
  Vecbase:  ftp://vectorbase.org/.../
  BettleBase:  Tribolium_Official_Gene_Sequences
  wFleaBase: http://wfleabase.org/release1/gene-predictions/
  SilkDB.org : ftp://silkworm.swu.edu.cn/pub/release_2.0/Gene/Glean_genes/
  
Daphnia true total (only used best 31952)
Daphnia pulex	37,329	37,466	NCBI Gnomon/wFleaBase, May 2007

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Developed at the Genome Informatics Lab of Indiana University Biology Department