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BLAT Alignments of NCBI RefSeq Genes   (All Genes and Gene Prediction Tracks)

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Data last updated at UCSC: 2022-10-20

Description

D. erecta transcripts from the NCBI RefSeq database were aligned against the D. erecta assembly using BLAT. The thicker boxes denote the coding regions within the transcripts and the thinner boxes denote the untranslated regions.

Methods

D. erecta transcripts were mapped against the D. erecta genome assembly using BLAT with the following parameters:

    -q=rna -fine -minScore=20 -stepSize=5

The transcript alignments are analyzed by pslReps using the following parameter:

    -minCover=0.15 -minAli=0.98 -nearTop=0.001

The alignments are then filtered by pslCDnaFilter using the following parameters:

    -minId=0.95 -minCover=0.15 -localNearBest=0.001 \
    -minQSize=20 -ignoreIntrons -repsAsMatch -ignoreNs -bestOverlap

References

Kent WJ. BLAT — the BLAST-like alignment tool. Genome Res. 2002 Apr;12(4):656-64.

The transcripts were obtained from the NCBI FTP site under the RefSeq assembly accession number GCF_003286155.1.