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  • How to annotate genes from gene prediction

    Hi,
    For a completly novel genome I used a gene prediction software called SNAP (http://korflab.ucdavis.edu/software.html) and it provided me a GFF and Fasta file (see below).

    SNAP's GFF:
    Code:
    XA8	SNAP	Einit	6161	7325	-5.800	-	.	XA8r-snap.4
    XA8	SNAP	Eterm	5974	6008	5.650	-	.	XA8r-snap.4
    SNAP's fasta:
    Code:
    >XA8-snap.4
    MAAHPPTLLDRAYGVNNIKSHIPIILDNNDHNYDAWRELLLTHCQSFEVA
    GHLDGTLLPTDDNDQLWIKRDGLVKLWLYGTISKDLFRSVFKTGGTSREI
    WTRIENYFRDNKEARAIRLDHELRNKTIGDLTIHAYRQDLKSISELLANV
    ESPVSERTLVTYMINGLSAKFDNIINVIMHRQPFPTFEQARSMLILEEER
    LNKGDKSPLVKDSPSSDKVLNVSATSQPPATTQQPQQQQRFYNNRGSKRN
    NRGRGRNYNNNQRPMYNQWGVPFWPNAYSFWGNQQQAPWGQQQFNNQGIL
    GPRPSQQAHQVQTQGQFPSAAPFVPTTDFASAFNTMTLTDPTDHQWYMDS
    GATAHLTNNPGNLKSILNTGTKQTVKVANGDIIPITKTGPSNSTDNSPQ*
    In next step I used the SNAP's fasta file to Blastp against UniRef90 and I have got the following XML file:

    Code:
    <?xml version="1.0"?>
    <!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "http://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.dtd">
    <BlastOutput>
      <BlastOutput_program>blastp</BlastOutput_program>
      <BlastOutput_version>BLASTP 2.2.26+</BlastOutput_version>
      <BlastOutput_reference>Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&amp;auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), &quot;Gapped BLAST and PSI-BLAST: a new generation of protein database search programs&quot;, Nucleic Acids Res. 25:3389-3402.</BlastOutput_reference>
      <BlastOutput_db>/sw/db/uniprot/uniref90</BlastOutput_db>
      <BlastOutput_query-ID>Query_1</BlastOutput_query-ID>
      <BlastOutput_query-def>XA8-snap.1</BlastOutput_query-def>
      <BlastOutput_query-len>96</BlastOutput_query-len>
      <BlastOutput_param>
        <Parameters>
          <Parameters_matrix>BLOSUM62</Parameters_matrix>
          <Parameters_expect>1e-05</Parameters_expect>
          <Parameters_gap-open>11</Parameters_gap-open>
          <Parameters_gap-extend>1</Parameters_gap-extend>
          <Parameters_filter>F</Parameters_filter>
        </Parameters>
      </BlastOutput_param>
      <BlastOutput_iterations>
        <Iteration>
          <Iteration_iter-num>4</Iteration_iter-num>
          <Iteration_query-ID>Query_4</Iteration_query-ID>
          <Iteration_query-def>XA8-snap.4</Iteration_query-def>
          <Iteration_query-len>400</Iteration_query-len>
          <Iteration_hits>
            <Hit>
              <Hit_num>1</Hit_num>
              <Hit_id>UR090:UniRef90_Q9FX16</Hit_id>
              <Hit_def>F12G12.10 protein n=1 Tax=Arabidopsis thaliana RepID=Q9FX16_ARATH</Hit_def>
              <Hit_accession>UR090:UniRef90_Q9FX16</Hit_accession>
              <Hit_len>308</Hit_len>
              <Hit_hsps>
                <Hsp>
                  <Hsp_num>1</Hsp_num>
                  <Hsp_bit-score>278.1</Hsp_bit-score>
                  <Hsp_score>710</Hsp_score>
                  <Hsp_evalue>1.87694e-87</Hsp_evalue>
                  <Hsp_query-from>10</Hsp_query-from>
                  <Hsp_query-to>290</Hsp_query-to>
                  <Hsp_hit-from>8</Hsp_hit-from>
                  <Hsp_hit-to>286</Hsp_hit-to>
                  <Hsp_query-frame>0</Hsp_query-frame>
                  <Hsp_hit-frame>0</Hsp_hit-frame>
                  <Hsp_identity>146</Hsp_identity>
                  <Hsp_positive>192</Hsp_positive>
                  <Hsp_gaps>10</Hsp_gaps>
                  <Hsp_align-len>285</Hsp_align-len>
                  <Hsp_qseq>DRAYGVNNIKSHIPIILDNNDHNYDAWRELLLTHCQSFEVAGHLDGTLLPTDDNDQLWIKRDGLVKLWLYGTISKDLFRSVFKTGGTSREIWTRIENYFRDNKEARAIRLDHELRNKTIGDLTIHAYRQDLKSISELLANVESPVSERTLVTYMINGLSAKFDNIINVIMHRQPFPTFEQARSMLILEEERLNKGDK-SPLVKDSPSSDKVLNVSATSQPPATT-QQPQQQQRFYNNRGSKRN-NRGRGRNYNNNQRPMYNQWGV-PFWPNAYSFWGNQQQAPWG</Hsp_qseq>
                  <Hsp_hseq>EQIYGVSNIKSHIPVMLDIEESNYDAWRELFLTHCLSFDVMGHIDGTLLPTNANDVNWQKRDGIVKLSLYGTLTPKQFQGSFVTSSTSRDIWLRIKNQFRNNKDARALRLDSELRTKDIGDMRVADYYRKMKKLADSLRNVDVPVTDRNLVMYVLNGLNPKFDNIINVIKHRQPFPSFDDAATMLQEEEDRLKRAIKPNPTHVDHSSSSTVL--ACSEAPPVTNFQRSGGNQMGYRGRGRGNNIFRGRGGRFSYYNMPTFNSWNRPPFYQNSYQMWNH----PWG</Hsp_hseq>
                  <Hsp_midline>++ YGV+NIKSHIP++LD  + NYDAWREL LTHC SF+V GH+DGTLLPT+ ND  W KRDG+VKL LYGT++   F+  F T  TSR+IW RI+N FR+NK+ARA+RLD ELR K IGD+ +  Y + +K +++ L NV+ PV++R LV Y++NGL+ KFDNIINVI HRQPFP+F+ A +ML  EE+RL +  K +P   D  SS  VL  + +  PP T  Q+    Q  Y  RG   N  RGRG  ++    P +N W   PF+ N+Y  W +    PWG</Hsp_midline>
                </Hsp>
              </Hit_hsps>
            </Hit>
    ...
    How would be possible to generate a GFF3 or GTF file with annotations for SNPeff (http://snpeff.sourceforge.net/)?


    Is there any good annotation pipeline avaible?

    Thank you in advance.
    Last edited by mictadlo; 09-17-2013, 06:00 PM.

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