Hello guys, I have downloaded Tribolium castaneum transcripts in fasta format from NCBI (http://www.ncbi.nlm.nih.gov/genome/?term=Tribolium%20castaneum), what is the difference between these sequences and assembled transcriptome sequences generated from RNA-seq? can both of them stands for protein codding sequences? What is the difference with the transcripts (mRNA) sequences downloaded from NCBI and RNA-seq assembled sequences?
Tribolium assembly was generated by Baylor using Sanger sequencing. The supplementary material indicates that the EST's were separately sequenced.
In principle the transcripts assembled using Sanger sequencing should be similar to ones generated by RNAseq (provided the assembly programs worked well in both cases). RNAseq data likely presents a deeper sampling of the transcriptome (because of the differences in technology) and may have better representation of transcripts.