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Among the collected markers, some were assembled by several ESTs using the Phrap program (http://www.phrap.org/index.html).html
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In contrast, a phenylalanine residue is encoded at that position by several ESTs from cvs Cheyenne and Glenlea (not shown).
We performed gene ontology (GO) analysis on 6132 genes identified by 454 ESTs using GOstat [ 14].
PipeBLASTN was followed by in silico extension of the remaining placenta ESTs using public domain cattle ESTs.
Putative dipteran homologs were found by comparing D. melanogaster mORFs to 666,153 NCBI ESTs using tBLASTn.
Two positive clones were sequenced to identify ORFs based on similarities to known proteins, and to ESTs using bioinformatics, and manually by a curator.
For such clusters, sequencing errors associated with individual ESTs will generally be corrected by overlapping ESTs used in the consensus sequence.
Contigs of several ESTs were assembled using Sequencher 4.5 (GeneCodes) and examined for quality before export and conceptual translation of consensus sequences.
In our test dataset, the 35363 sampled ESTs used were submitted by more than 800 research groups, while the 575 contaminated ESTs were submitted by 100 of them.
Further investigation using the UCSC genome browser (http://genome.ucsc.edu) identified several ESTs (spliced and unspliced) originating from the transcribed region identified on chromosome 9 (Figure S6A).
Several ESTs for SuSy genes were present.
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