Description
These tracks feature annotations of genes on each contig or pseudochromosome.
For more information on assemblies please see the description page.
Methods
Initial sets of annotations (labeled 'MAKER2') were united using the MAKER2 pipeline v2.31.8 [Mark and Yandell et al., 2011].
To restore strandard gene names, genes found with this pipeline were divided into novel and known ones with an in-house python script available at github. This script employs a renaming table produced with proteinortho [Lechner et al., 2011] by clustering the whole sets of ORFs from the reference strain (S288C) and the strain analyzed. Tracks with renamed genes are labeled 'MAKER 2 renamed'.
Please note that standart yeast ORF names (e.g. YBR043C) are indexed and can be used for searching.
References
Holt C, Yandell M. MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects. BMC Bioinformatics [Internet]. 2011 Jan [cited 2015 Mar 9];12(1):491. Available from: http://www.biomedcentral.com/1471-2105/12/491
Lechner M, Findeiss S, Steiner L, Marz M, Stadler PF, Prohaska SJ. Proteinortho: detection of (co-)orthologs in large-scale analysis. BMC Bioinformatics [Internet]. BioMed Central Ltd; 2011 Jan 28 [cited 2015 Nov 12];12(1):124. Available from: http://www.biomedcentral.com/1471-2105/12/124
Contacts
If you have questions please contact Polina Drozdova at drozdovapb@gmail.com
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