(iii) Prediction based on transcript sequences: The assembled transcriptome sequences were aligned to the genome assembly using BLAT (Version 34) using the parameters identity ≥ 0.98 and coverage ≥ 0.98 to generate spliced alignments.
Although our assembly appears to be of reasonable quality based on transcript metrics such as N50, mean length, and coverage, determining whether transcripts are in fact correctly assembled poses a particular challenge.
GLEAN uses transcript alignments to support splice predictions, but does not merge or split genes based on transcript alignments, while MAKER2 creates gene models that best agree with transcript alignments, and works best with highly reliable transcript assemblies.
A database was constructed based on transcripts obtained from the koala mammary gland (sequencing and assembly described below).
Based on the transcript assembly and subsequently primer walking, 433 full-length cDNA sequences were successfully generated.
In addition, based on the transcript assembly described above, we found that cucumber ESTs generated in this study covered ~70% (2,625/3,772, Table 2) of genes derived from GenBank ESTs and mRNAs which were generated from various different tissues including flower, fruit and leaf.
Quotations are based on transcripts provided by Factbase.
Some are based on transcripts and audio recordings, others are stories recited through the generations.
We conducted the re-annotation of the IPO323 genome using a pipeline that identifies the most probable gene models based on information from transcript assemblies, homology searches, and ab initio gene predictors (Haas et al. 2011).
Based on TIGR plant transcript assemblies (TIGR TA), more than 1,000 ESTs or cDNA sequences are available for 254 plant species reaching a sum of 10,974,563 ESTs (Current Release Summary, update July 2007).
