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Integrating Genetics and Genomics to Advance Soybean Research

Reference Report for RTN20161130.1
Title:Functional annotation of soybean gene models
Authors:No authors listed
Source:Personal Communication
Abstract:(1) GlymaID from Gmax version 2.0. Only primary predicted proteins were included in analyses. For more information on Gmax2.0 cDNAs see http://phytozome.jgi.doe.gov/pz/portal.html#!info?alias=Org_Gmax. (2) Top Uniref100 BLASTP Hit. Match determined via BLASTP of Gmax2.0 primary proteins against Uniref100 (version 03/27/2014). E-value for the top high scoring pair(HSP) is indicated. Top Uniref100 percent coverage determined by dividing the length of the top HSP by the length of the hit sequence. (3) Top Descriptive Uniref100 BLASTP Hit. The BLAST report generated above (2) was parsed to eliminate uninformative hits. Hits including the words uncharacterized, putative, related, predicted, orf, expressed or containing Arabidopsis or Rice gene identifiers (AtXgXXXXX, OsXXgXXXXX) were ignored. E-value for the top high scoring pair(HSP) is indicated. Top Uniref100 percent coverage determined by dividing the length of the top HSP by the length of the hit sequence. (4) Top Arabidopsis (TAIR10) BLASTP Hit (4). Match determined via BLASTP of Gmax2.0 primary proteins against Arabidopsis thaliana proteins (TAIR10). For additional details see www.arabidopsis.org. E-value for the top high scoring pair(HSP) is indicated. Percent coverage determined by dividing the length of the top HSP by the length of the hit sequence. (5) Gene Ontology Biological Process IDs. GO Biological Process IDs were assigned to each Gmax2.0 ID using the GO terms associated with the Top TAIR10 BLASTP Hit (4). The annotation information was obtained from TAIR v 10 (03/27/14). Descriptions for the GO terms are also provided. (6) Gene Ontology Molecular Function IDs. GO Molecular Function IDs were assigned to each Gmax2.0 ID using the GO terms associated with the Top TAIR10 BLASTP Hit (4). The annotation information was obtained from TAIR v. 10 (03/27/14). Descriptions for the GO terms are also provided. (7) Gene Ontology Cellular Component IDs. GO Cellular Component IDs were assigned to each Gmax2.0 ID using the GO terms associated with the Top TAIR10 BLASTP Hit (4). The annotation information was obtained from TAIR v 10 (03/27/14). Descriptions for the GO terms are also provided. (8) PFAM IDs and descriptions were assigned by Phytozome. For more information see http://phytozome.jgi.doe.gov/pz/portal.html#!info?alias=Org_Gmax. (9) PANTHER IDs and descriptions were assigned by Phytozome. For more information see http://phytozome.jgi.doe.gov/pz/portal.html#!info?alias=Org_Gmax. (10) KOG IDs and descriptions were assigned by Phytozome. For more information see http://phytozome.jgi.doe.gov/pz/portal.html#!info?alias=Org_Gmax.






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