Drosophila RefSeq Transcripts Track Settings
 
BLAT Alignment of Drosophila RefSeq Transcripts   (All Genes and Gene Prediction Tracks)

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Description

Drosophila transcripts from the NCBI RefSeq database were aligned against the D. pseudoobscura DpseGB3 assembly using BLAT. The thicker boxes denote the coding regions within the transcripts and the thinner boxes denote the untranslated regions.

Methods

RefSeq transcripts were mapped against the D. pseudoobscura genome assembly using BLAT with the following parameters: -repeats=lower -q=rnax -t=dnax -mask=lower

The transcript alignments are analyzed by pslReps using the following parameter: -minAli=0.25

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

    -minId=0.35 -minCover=0.15 -localNearBest=0.010 \
    -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 following RefSeq assembly accession numbers:

SpeciesAssembly NameRefSeq Accession
Drosophila melanogasterRelease 6 plus ISO1 MTGCF_000001215.4
Drosophila mauritianaASM438214v1GCF_004382145.1
Drosophila sechelliaASM438219v2GCF_004382195.2
Drosophila simulansPrin_Dsim_3.1GCF_016746395.2
Drosophila yakubaPrin_Dyak_Tai18E2_2.1GCF_016746365.2
Drosophila santomeaPrin_Dsan_1.1GCF_016746245.2
Drosophila teissieriPrin_Dtei_1.1GCF_016746235.2
Drosophila erectaDereRS2GCF_003286155.1
Drosophila ficusphilaASM1815226v1GCF_018152265.1
Drosophila suzukiiDsuz_RU_1.0GCF_037355615.1
Drosophila subpulchrellaRU_Dsub_v1.1GCF_014743375.2
Drosophila biarmipesRU_DBia_V1.1GCF_025231255.1
Drosophila takahashiiASM1815269v1GCF_018152695.1
Drosophila eugracilisASM1815383v1GCF_018153835.1
Drosophila rhopaloaASM1815211v1GCF_018152115.1
Drosophila elegansASM1815250v1GCF_018152505.1
Drosophila gunungcolaDgunungcola_SK_2GCF_025200985.1
Drosophila kikkawaiASM1815253v1GCF_018152535.1
Drosophila serrataDser1.1GCF_002093755.2
Drosophila bipectinataASM1815384v1GCF_018153845.1
Drosophila ananassaeASM1763931v2GCF_017639315.1
Drosophila pseudoobscuraUCI_Dpse_MV25GCF_009870125.1
Drosophila persimilisDperRS2GCF_003286085.1
Drosophila mirandaD.miranda_PacBio2.1GCF_003369915.1
Drosophila guancheDGUA_6GCF_900245975.1
Drosophila subobscuraUCBerk_Dsub_1.0GCF_008121235.1
Drosophila obscuraASM1815110v1GCF_018151105.1
Drosophila willistoniUCI_dwil_1.1GCF_018902025.1
Drosophila arizonaeASM165402v1GCF_001654025.1
Drosophila mojavensisASM1815372v1GCF_018153725.1
Drosophila navojoaUFRJ_Dnav_4.2GCF_001654015.2
Drosophila hydeiDhydRS2GCF_003285905.1
Drosophila virilisDvirRS2GCF_003285735.1
Drosophila novamexicanaDnovRS2.1GCF_003285875.2
Drosophila montanaASM3504440v1GCF_035044405.1
Drosophila grimshawiASM1815329v1GCF_018153295.1
Drosophila albomicansASM965048v2GCF_009650485.2
Drosophila nasutaASM2355853v2GCF_023558535.2
Drosophila sulfurigaster albostrigataASM2355843v2GCF_023558435.1
Drosophila innubilaUK_Dinn_1.0GCF_004354385.1
Drosophila busckiiASM1175060v1GCF_011750605.1