Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • 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.

Latest Articles

Collapse

  • seqadmin
    Strategies for Sequencing Challenging Samples
    by seqadmin


    Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...
    03-22-2024, 06:39 AM
  • seqadmin
    Techniques and Challenges in Conservation Genomics
    by seqadmin



    The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.

    Avian Conservation
    Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...
    03-08-2024, 10:41 AM

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by seqadmin, Yesterday, 06:37 PM
0 responses
11 views
0 likes
Last Post seqadmin  
Started by seqadmin, Yesterday, 06:07 PM
0 responses
10 views
0 likes
Last Post seqadmin  
Started by seqadmin, 03-22-2024, 10:03 AM
0 responses
51 views
0 likes
Last Post seqadmin  
Started by seqadmin, 03-21-2024, 07:32 AM
0 responses
67 views
0 likes
Last Post seqadmin  
Working...
X