Words similar to genscan
Example sentences for: genscan
How can you use “genscan” in a sentence? Here are some example sentences to help you improve your vocabulary:
The exon index is an integrated table generated by a Sybase relational database, consisting of chromosome number, fingerprinted contig (FPC) ID, FPC contig order, BAC contig ID, BAC contig order, BAC contig orientation, starting position of exon on BAC contig, end position of exon on BAC contig, exon orientation, transcript orientation (available from GenBank, IMAGE, UniGene, HINT and dbEST), evidence (transcript, protein, gene prediction, ORF, Pfam), database name (Table 1), feature (poly(A) signal, CpG island, Genscan boundary), starting position on exon (or feature), end position on exon (or feature), score (BlastN, BlastX).
To balance the false-positive and false-negative rates of GENSCAN, we used an empirical prediction score as a threshold, as done previously [ 44].
This pipeline aligns Drosophila ESTs, cDNA sequences, and other sequences in GenBank using sim4 [ 53], performs DNA and protein sequence similarity searches of the GenBank and SwissProt/TrEMBL databases using BLASTX and TBLASTX, and executes the gene-prediction algorithms Genie [ 68] and Genscan [ 69].
The following criteria were used to identify gene boundaries: known 5' or 3' UTR sequences in UTR-DB; full-length cDNAs in HTDB; exons in partial ORFs as possible boundaries of coding regions; exons without continuous ORFs as additional UTR sequences; CpG islands; and gene boundaries predicted by Genscan.
In the absence of other supporting evidence for a gene, we used GENSCAN predictions only when at least one exon had a score > 45; this is a stringent threshold, as 21% of the genes in Release 3 with full-length cDNA evidence do not contain any exons scoring > 45.
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