• Anonymous
  • Login

Search:  Display ?

Assembly/Version:  Chr:  Start:  End: Display:

CpGAT - A Comprehensive Pipeline for Genome Annotation

CpGAT is a comprehensive tool for annotating genomic regions up to 500 kilobases. CpGAT uses EVM (EVidence Modeler) to evaluate GenomeThreader protein/transcript spliced alignments together with ab initio gene finder results (BGF, GeneMark, and Augustus). In addition, some PASA functions are used to aggregate splice variant models. Output file formats include GFF3, Gbrowse text, and FASTA (transcript, CDS and translation). The gene models are also displayed in PlantGDB's genome browser and yrGATE annotation tool. Click to view CpGAT Schema (Liu et al., 2010, Manuscript in Preparation)

Note: CpGAT is also available at our BIoExtract website. BioExtract publishes an external link to access the CpGAT tool (login account required)

More Information on CpGAT...

Step 0: To use existing xGDB alignments (faster), check this box: and skip to step 5 below.

Step 1: If not autofilled, paste genomic DNA sequences here:



...or upload genomic sequences from


Step 2: Select protein dataset(s) to use for spliced alignment: ?

Species Protein
Dataset  
Select
Arabidopsis_thaliana:ATpep
Brachypodium_distachyon:BDpep
Brassica_rapa:BRpep
Carica_papaya:CPpep
Chlamydomonas_reinhardtii:CRpep
Cucumis_sativus:CSpep
Glycine_max:GMpep
Lotus_japonicus:LJpep
Manihot_esculenta:MEpep
Mimulus_guttatus:MGpep
Medicago_truncatula:MTpep
Oryza_sativa:OSpep
Prunus_persica:PEpep
Physcomitrella_patens:PPpep
Populus_trichocarpa:PTpep
Ricinus_comunis:RCpep
Sorghum_bicolor:SBpep
Setaria_italica:SIpep
Volvox_carteri:VVpep
Zea_mays:ZMpep

...or upload proteins from


Step 3: Select transcript datset(s) to use for spliced alignment: ?

Species  cDNA   H.T.
 cDNA 
 EST     PUT   
Monocots (Liliopsida):
Brachypodium_distachyon
Hordeum_vulgare_subsp__vulgare
Hordeum_vulgare_subsp__spontaneum
Hordeum_vulgare
Oryza_sativa
Oryza_sativa_Indica_Group
Oryza_sativa_Japonica_Group
Sorghum_bicolor
Triticum_aestivum
Zea_mays
All Monocots
Dicots (eudicotyledons)
Arabidopsis_thaliana
Brassica_rapa_subsp__pekinensis
Brassica_rapa
Carica_papaya
Gossypium_hirsutum
Glycine_max
Lotus_japonicus
Medicago_truncatula
Prunus_persica
Populus_trichocarpa
Solanum_lycopersicum
Vitis_vinifera
Cucumis_sativus
Manihot_esculenta
Mimulus_guttatus
Ricinus_comunis
All Dicots
Other Species
Chlamydomonas_reinhardtii
Volvox_carteri
Physcomitrella_patens
Physcomitrella_patens_subsp__patens
All Species


...or upload transcripts from


Step 4: Select splice site model for protein/transcript spliced alignment:

       GenomeThreader: 

Step 5: Select Repeat Database for masking repeats:

       Repeat Database: 

Step 6: Select species model for ab initio gene finders, or check box to skip:

        BGF:             Skip BGF: 

        Augustus:   Skip Augustus: 

        GeneMark:   Skip GeneMark: 

Step 7: Click for additional CpGAT options (hover for description):

 Skip Mask:  Relax UniRef:  Skip PASA:  Skip BLAST:

Step 8:



Loading Help Page...Thanks for your patience!

Loading Video...Thanks for your patience!

Loading Image...Thanks for your patience!