exonerate根据蛋白序列预测基因组中的基因（外显子和内含子区域）

exonerate --bestn 1 --score 90 --exhaustive yes --forcegtag TRUE --model protein2genome /Pro_Hc_g3V-D3.fa Pro_Hc_g3V-D3.fa -
-ryo \nSugar  block: %S\nCigar block: %C\nEquivalenced mismatches: %em\nEquivalenced similarity: %es(%ps)\nGene orientation: %g\nCDS region: %tcb-%tce\nAligned reginon: %tab-%tae\n>%ti(%tab-%tae
)\n%tcs\n --showtargetgff TRUE]


         Query: Pro_Hc_g3V-D3
        Target: Pro_Hc_g3V-D3##HiC_scaffold_14##46807373##46930452  HiC_scaffold_14:46807373-46930452:+  len=123080
         Model: protein2genome:local
     Raw score: 3110
   Query range: 0 -> 665
  Target range: 11997 -> 111083

      1 : ArgSerSerThrGlyHisGlnHisLeuLeuIleGluValAlaSerValProLeuTyrI :     20
          !.!|||! !  !.!!|||||||||||||||:!!|||||||||||||||||||||  !|
          HisSerIleCysSerHisGlnHisLeuLeuLeuGluValAlaSerValProLeuProI
  11998 : CATTCTATTTGCAGTCACCAGCACCTGCTGTTAGAAGTAGCTTCTGTTCCTCTGCCTA :  12055

     21 : leSerGluThrHisGlnAspPheLysMetThrValLysGluLysGluAspLysValLe :     39
          ||||||||!:!|||!!.|||||||||||||||||||||||||||||||||:!!|||||
          leSerGluSerHisHisAspPheLysMetThrValLysGluLysGluAspGlnValLe
  12056 : TCTCTGAAAGCCATCACGATTTCAAGATGACCGTCAAAGAGAAGGAAGACCAAGTTTT :  12112

     40 : uProLeuPheGluGlnLeuMetThrLeuThrLysLysGlnLeuProValAspGlnArg :     58
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
          uProLeuPheGluGlnLeuMetThrLeuThrLysLysGlnLeuProValAspGlnArg
  12113 : GCCACTGTTCGAGCAGTTGATGACCCTCACCAAAAAGCAGCTGCCTGTAGATCAAAGG :  12169

     59 : AspPro***ArgLeuAlaHisPheGlyGluIleProArgGlyThrLeuPheAspCysP :     78
          ||||||   |||||||||||||||||||||||||||||||||||||||||||||||||
          AspPro---ArgLeuAlaHisPheGlyGluIleProArgGlyThrLeuPheAspCysP
  12170 : GACCCA---AGACTCGCCCACTTCGGGGAAATTCCCAGAGGAACACTCTTCGACTGCT :  12226

     79 : heHisGluValHisLeuHisGluAlaThrGluLeuPheLysValLeuTyr{A}  >>> :     95
          ||||||||  !|||||||||||||||||||||||||||||||||||||||{|}
          heHisGluLysHisLeuHisGluAlaThrGluLeuPheLysValLeuTyr{A}++
  12227 : TCCACGAGAAACACCTTCATGAAGCAACCGAACTCTTTAAGGTTTTGTAT{G}gt... :  12280

     96 : > Target Intron 1 >>>>  {la}AlaAsnAspPheAspAspPheIleHisLeu :    105
                75724 bp          {||}||||||||||||||||||||||||||||||
                                ++{la}AlaAsnAspPheAspAspPheIleHisLeu

=========
    635 : ProPheAspArgProLeuThrAlaHisSerGluAlaGluLeuLeuThrAspAsnMetV :    654
          |||||||||||||||:!!||||||||||||||||||||||||||||||||||||||||
          ProPheAspArgProMetThrAlaHisSerGluAlaGluLeuLeuThrAspAsnMetV
 110989 : CCCTTCGACAGGCCCATGACAGCCCACAGCGAGGCAGAGCTCCTCACAGACAACATGG : 111048

    655 : alPheThrAspValLysIleLysPheLeuAsp*** :    665
          |||||||||||||||||||||||||||||||||||
          alPheThrAspValLysIleLysPheLeuAsp***
 111049 : TCTTCACCGACGTCAAAATCAAGTTCTTGGATTAA : 111083


# seqname source feature start end score strand frame attributes
#
Pro_Hc_g3V-D3##HiC_scaffold_14##46807373##46930452   exonerate:protein2genome:local  gene    11998   111083  3110    +       .       gene_id 0 ; sequence DesPro_Hc_g3V-D3 ; gene_orientation +
Pro_Hc_g3V-D3##HiC_scaffold_14##46807373##46930452   exonerate:protein2genome:local  cds     11998   12277   .       +       .
Pro_Hc_g3V-D3##HiC_scaffold_14##46807373##46930452   exonerate:protein2genome:local  exon    11998   12277   .       +       .       insertions 0 ; deletions 1
Pro_Hc_g3V-D3##HiC_scaffold_14##46807373##46930452   exonerate:protein2genome:local  splice5 12278   12279   .       +       .       intron_id 1 ; splice_site "GT"
Pro_Hc_g3V-D3##HiC_scaffold_14##46807373##46930452   exonerate:protein2genome:local  intron  12278   88001   .       +       .       intron_id 1
Pro_Hc_g3V-D3##HiC_scaffold_14##46807373##46930452   exonerate:protein2genome:local  splice3 88000   88001   .       +       .       intron_id 0 ; splice_site "AG"

HiC_scaffold_14##46807373##46930452(11997 -> 111083)的含义是在HiC_scaffold_14上的##46807373##46930452区间上，从第11997 开始匹配->到 第111083结束（Target range），中间会预测出外显子和内含子位置。那么这个基因实际上是从第（46807373+11997）位到第（46807373+111083）

这是一条预测正向转录的基因，程序设置了在原先比对的基础上延伸12000bp，当遇到可以补全的地方，则会选入预测结果，如这里的11997则是因为向前增加了3个碱基，如果没采纳应该默认是12000。

image.png

image.png

基因 DNA 分为编码区和非编码区，编码区包含外显子和内含子，一般非编码区具有基因表达的调控功能，如启动子在非编码区。编码区则转录为 mRNA 并最终翻译成蛋白质。
外显子和内含子都被转录到 mRNA 前体 hnRNA 中，当 hnRNA 进行剪接变为成熟的 mRNA 时，内含子被切除，而外显子保留。实际上真正编码蛋白质的是外显子，而内含子则无编码功能。
内含子存在于DNA 中，在转录的过程中，DNA 上的内含子也会被转录到前体 RNA 中，但前体 RNA 上的内含子会在 RNA 离开细胞核进行翻译前被切除。

https://en.wikipedia.org/wiki/Intron