Current State of Annotation

The annotation process of some of the Tallapoosa darter scaffolds began in September 2013 by the inaugural annotation team at the University of West Georgia. The annotation process utilized the red line annotation workflow on the DNA Subway website. A number of 20 kb scaffolds were annotated as were a number of scaffolds that contained single copy genes homologous to full length Perca flavescens mRNAs.

In November 2013, Tallapoosa darter scaffolds greater than 8,000 nucleotides in length along with  some shorter scaffolds that contained the Perca flavescens mRNA homologous genes  and the associated fgenesh derived gene models for all these scaffolds were imported into WebApollo. Students in the genetics class at the University of West Georgia annotated a number of 10,000 nucleotide long scaffolds at the end of the fall semester utilizing the workflow described in the Annotations Process description (link in navigation bar on left). The annotations created in DNA subway are being transferred into WebApollo.

In general, while some scaffolds do not contain any protein coding sequences, most of the scaffolds in these size ranges contain at least a portion of a protein coding gene.

The following is a listing of some of the annotated scaffolds. More will be added as the annotations are verified.

scaffold40_size20880
scaffold44_size44559
scaffold46_size20421
scaffold156_size20360
scaffold177_size20491
scaffold192_size20319
scaffold234_size47437
scaffold297_size42957
scaffold617_size39554
scaffold702_size20676
scaffold777_size20668
scaffold798_size20793
scaffold822_size20226
scaffold1375_size10702
scaffold2201_size9465 (Perca mRNA homologous gene)
scaffold4148_size47067
scaffold11666_size10646 (Perca mRNA homologous gene)
scaffold43749_size3944 (Perca mRNA homologous gene)
scaffold73143_size4403 (Perca mRNA homologous gene)
scaffold92874_size2518 (Perca mRNA homologous gene)
scaffold98292_size1752 (Perca mRNA homologous gene)
scaffold137950_size1263 (Perca mRNA homologous gene)

Combined scaffolds by homology to Perca mRNA:
scaffolds_AY332490
scaffolds_AY332493
scaffolds_EU073713
scaffolds_EU81834
scaffolds_FJ826534
scafolds_FJ804426