This track displays the alignment of N2 (WS230) coding transcripts to the CB4856 reference genome using blat. As such, any gene models seen here should serve as nothing more than an approximation of those in the CB4856 genome: in regions of high similarity between CB4856 and N2, this track is likely to reflect CB4856 coding genes. UTRs were not included in the transcript sequences used for alignment and are not integrated into these gene models.
Please note that aligning N2 coding transcripts back to N2 (i.e. back to the reference from which they are derived) results in 96.1% recovery of the gene model by this method. The accuracy of N2 gene models aligned to the CB4856 reference is certain to be less accurate than this, given the differences between the two geneomes.
Display Conventions and Configuration
N2 coding sequence alignments to the CB4856 reference genome are presented in bed format, with default display mode "pack". Exons and introns should be visible for each transcript model, with the strand clearly displayed with arrows in intronic regions.
GFF3 annotations from Wormbase release WS230 were downloaded and coordinates for annotated mRNA transcripts were obtained. Reference sequence for all fields annotated as "Coding_transcript" were catenated and converted to the coding strand; UTRs were excluded, which may contribute to incorrect alignments where the first/last intron of a transcript is very near the start/stop codon within the first/last exon.
Full mRNA transcripts were aligned to the CB4856 reference genome with blat version 35x1 (available here), generating a psl file for each transcript. The top-scoring alignment was converted to bed format, provided the entire length of the transcript mapped to the reference. Of 31249 transcripts, 29368 aligned to the reference in this way (94%), with 1603 incompletely aligning and 278 failing to produce any alignment.
Please feel free to contact Owen Thompson with any questions and/or concerns regarding this or other tracks.
Thanks to Wormbase for providing gff3 annotations of the N2 reference genome. Thanks also to Jim Kent at the Department of Biomolecular Engineering at UCSC for providing blat.
Harris TW, Baran J, Bieri T, et al. WormBase 2014: new views of curated biology. Nucleic Acids Res. 2014;42(Database issue):D789-93. PMID 24194605.
Kent WJ. BLAT--the BLAST-like alignment tool. Genome Res. 2002;12(4):656-64. PMID 11932250.