Geneid Gene Predictions (mRNA_geneid-CM002916_4)
  Position: CM002916:201051-272329
Genomic Size: 71279
Strand: +
Gene Symbol: geneid-CM002916_4
CDS Start: unknown (coding, but not known)
CDS End: unknown (coding, but not known)

Links to sequence:

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Data last updated at UCSC: 2022-10-20

Description

This track shows gene predictions from the geneid program developed by Roderic Guigó's Computational Biology of RNA Processing group which is part of the Centre de Regulació Genòmica (CRG) in Barcelona, Catalunya, Spain.

Methods

Geneid is a program to predict genes in anonymous genomic sequences designed with a hierarchical structure. In the first step, splice sites, start and stop codons are predicted and scored along the sequence using Position Weight Arrays (PWAs). Next, exons are built from the sites. Exons are scored as the sum of the scores of the defining sites, plus the the log-likelihood ratio of a Markov Model for coding DNA. Finally, from the set of predicted exons, the gene structure is assembled, maximizing the sum of the scores of the assembled exons.

Credits

Thanks to Computational Biology of RNA Processing for providing these data.

References

Blanco E, Parra G, Guigó R. Using geneid to identify genes. Curr Protoc Bioinformatics. 2007 Jun;Chapter 4:Unit 4.3. PMID: 18428791

Parra G, Blanco E, Guigó R. GeneID in Drosophila. Genome Res. 2000 Apr;10(4):511-5. PMID: 10779490; PMC: PMC310871