Contributions of Zea mays subspecies mexicana haplotypes to modern maize..
Ning Yang, Xi-Wen Xu, Rui-Ru Wang, Wen-Lei Peng, Lichun Cai, Jia-Ming Song, Wenqiang Li, Xin Luo, Luyao Niu, Yuebin Wang, Min Jin, Lu Chen, Jingyun Luo, Min Deng, Long Wang, Qingchun Pan, Feng Liu, David Jackson, Xiaohong Yang, Ling-Ling Chen, Jianbing Yan
The length of scaffold which takes the sum length (summing from longest to shortest scaffold) past 50% of the total assembly size.
The length of contig which takes the sum length (summing from longest to shortest contig) past 50% of the total assembly size.
A contig is a contiguous consensus sequence that is
derived from a collection of overlapping reads.
A scaffold is set of a ordered and orientated contigs
that are linked to one another by mate pairs of sequencing reads.
An integrated approach combining de novo prediction with evidence-based data (ESTs, protein homology and RNA-seq) analysis was employed by using the PASA and EVM pipeline. The predicted gene models from EVM were then updated by PASA assembly alignments. Gene functions were assigned according to the best alignment using BLASTP (E-value < 10-5) to the UniProt database. InterProScan was used to identify gene ontology terms, motifs, and domains of gene models.