Alignment of our cDNA contigs with predicted CDS also identified 78 genes, although not fully covered by our cDNA sequences, with 88 introns either missed by computer prediction or predicted incorrectly (Additional file 3).
The expression of Cyclin D1, FOXP1, FIH-1, pan-ERβ, NRP1 and CD99, predicted to be regulated by BRCA1 specific miRNAs by computer prediction algorithms, was assessed via immunohistochemistry in a cohort of 35 BRCandand 52 sporadic basal-like cancers.
Interestingly, by computer prediction, the 40 bp repeat seems to be able to form strong secondary structures.
This 8 amino acid insertion is not found in other TOX subfamily members or the human homologue C20ORF100, and can be explained by an error in the automated computer prediction of the end of the relevant exon.
Computer prediction of ligand binding was carried out using AutoDock Vina.
The changes match computer predictions of how the frozen north could respond to the buildup in the atmosphere of heat-trapping greenhouse gases, mainly carbon dioxide released by burning fossil fuels.
Others focus on computer predictions of miRNAs using EST or genomic sequencing data [8], [9].
Coding regions were assigned by a combination of computer prediction and similarity search.
RNA- and protein-encoding regions were assigned by a combination of computer prediction and similarity searches, as described previously.
The potential protein-encoding regions were assigned using a combination of computer prediction by the Glimmer program and similarity search, as described in Section 2. By taking into account sequence similarity to known genes and relative position, to avoid overlaps, the total number of putative protein-encoding genes assigned to the genome was 6312.
