BLAT Alignments of NCBI RefSeq Genes (XM_016180640)
  GenBank Record: XM_016180640

Item: XM_016180640
Score: 1000
Position: CM002916:270415-272664
Genomic Size: 2250
Strand: +
View DNA for this feature (DsimGB2/D. simulans)

Gene Symbol: LOC6724700

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Data last updated at UCSC: 2022-10-20

Description

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

Methods

D. simulans transcripts were mapped against the D. simulans 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_016746395.2.