The transcript assembly is essential for transcriptome studies trom next-generation sequencing data. However, there are still many faults of algorithms in the present assemblers, which should be largely improved in the future. According to the requirement of reference genome or not, the transcript assembly could be classified into the genome-guided and de novo methods. The two methods have different algorithms and implementation processes. The quality of assembled transcripts depends on a large number of factors, such as the PCR amplification, sequencing techniques, assembly algorithm and genome character. Here, we reviewed the present tools of transcript assembly and various indexes for assessing the quality of assembled transcripts, which would help biologists to determine which assembler should be used in their studies.
Algorithms ; Gene Expression Profiling ; Genome ; Genomics ; methods ; High-Throughput Nucleotide Sequencing ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; Transcriptome

Objective To examine the effect of aerobic exercise training on plasma metabolites in pre-diabetes mellitus(PDM)subjects.Methods Twenty-five PDM subjects were selected,and each 10 age-and sex-matched with normoglycemia and new-onset T2DM subjects were enrolled.PDM subjects underwent aerobic exercise(n=13)or health education (n=12) for 12 weeks.The aerobic exercise was con ducted 3 times/week,50 min/time at 40％-60％ of oxygen uptake reserve.Liquid chromatography-mass spectrometry(LC-MS)was used to analyze the spectrum of plasma metabolites.Principal component analysis was employed to study the differences in plasma metabolite profiles between subjects with different glycemic level and between PDM subjects before and after aerobic exercise.Results After training,the body fat percentage,2-hour plasma glucose,and low density lipoprotein cholesterol of PDM subjects reduced significantly(by 4.6％,16.22％ and 9.27％ on average).Comparison of plasma metabolizers in PDM subjects before and after exercise revealed 31 differential metabolites,with 25 metabolites such as phosphatidylcholine,lysophosphatidylcholines,sphingomyelin and betaine increasing,and 6 metabolites,such as oleic acid and cytosine decreasing.Conclusion Aerobic exercise has a marked effect on the plasma metabolites in PDM subjects.Phosphatidylcholine,lysophosphatidylcholines,sphingomyelin and oleic acid may be the potential biomarkers of aerobic exercise improving the glycolipid metabolism in PDM subjects.These findings can help us better understand the mechanism of aerobic exercise preventing T2DM diabetes.