Changes between Version 9 and Version 10 of UTGBMedaka/Track


Ignore:
Timestamp:
08/15/07 00:17:05 (18 years ago)
Author:
leo
Comment:

--

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  • UTGBMedaka/Track

    v9 v10  
    33[[PageOutline]]
    44== Chromosome Overview ==
    5 {{{
    6 #!html
    7 <img src="img/ChromosomeOverView.jpg" width="908" height="20" alt="ChromosomeOverView.jpg"/><br>
     5[[Image(img/ChromosomeOverView.jpg)]]
    86
    9 <p>
    10 This track shows the location of presently displayed scaffold on the chromosome. In the above image, for instance, the blue-colored box shows the position of scaffold100 on chromosome 6, which is represented in the yellow bar. Click on any position of this track will bring you to the <a href="#chr">chromosome view</a>. The next scaffolds are indicated at the both end of yellow bar.  Click on the scaffold name shown in light blue to move to the view of the corresponding scaffold.
    11 </p>
     7This track shows the location of presently displayed scaffold on the chromosome. In the above image, for instance, the blue-colored box shows the position of scaffold100 on chromosome 6, which is represented in the yellow bar. Click on any position of this track will bring you to the chromosome view. The next scaffolds are indicated at the both end of yellow bar.  Click on the scaffold name shown in light blue to move to the view of the corresponding scaffold.
    128
    13 <p><A Name="chr">Chromosome view</A></p>
    14 <img src="img/ChrView2.jpg" width="980" height="325" alt="ChrView.jpg"><br>
    15 <p>
    16 The relationship among chromosome, scaffolds and genetic markers is shown in this window. The initial view is very busy, however, you can zoom into any region. Click on the scaffold name and genetic marker name to see the corresponding scaffold and genetic marker information, respectively.</p>
    17 }}}
     9== Chromosome view ==
     10[[Image(img/ChrView2.jpg)]]
     11
     12The relationship among chromosome, scaffolds and genetic markers is shown in this window. The initial view is very busy, however, you can zoom into any region. Click on the scaffold name and genetic marker name to see the corresponding scaffold and genetic marker information, respectively.
    1813
    1914== MedakaTrasncripts ==
    2015
    21 {{{
    22 #!html
    23 <img src="img/MedakaTranscriptsSc150.jpg" width="902" height="143" alt="MedakaTranscriptsSc150.jpg"/>
    24 <br>
     16[[Image(img/MedakaTranscriptsSc150.jpg)]]
    2517
    26 <p>This track shows a total set of medaka transcripts from  <a href = "http://www.ncbi.nlm.nih.gov/UniGene/UGOrg.cgi?TAXID=8090">Unigne database build#19 </A>in ncbi. Transcripts are initially aligned using BLASTN and listed the scaffolds which show the best match. The final alignments were produced between transcrips and the selected scaffolds using sim4, a program to align cDNA and genomic DNA (ref. 1). In some case, transcripts are mapped to unexpectedlly huge region because of the low complexity sequences in the transcripts. We eliminated these regions when the mapped region is over 200 kb. 
    27 </p>
    28 <p>
     18This track shows a total set of medaka transcripts from [http://www.ncbi.nlm.nih.gov/UniGene/UGOrg.cgi?TAXID=8090 Unigne database build#19] in ncbi. Transcripts are initially aligned using BLASTN and listed the scaffolds which show the best match. The final alignments were produced between transcrips and the selected scaffolds using sim4, a program to align cDNA and genomic DNA (ref. 1). In some case, transcripts are mapped to unexpectedlly huge region because of the low complexity sequences in the transcripts. We eliminated these regions when the mapped region is over 200 kb. 
     19
    2920Black-colored boxes indicate aligned regions and bars indicate gaps. Arrows indicate the transcription directions.  Click on each transcript opens a link to the information in the NCBI nucleotide database.
    30 </P>
    31 <p>
     21
    3222ESTs and mRNAs are represented by the clone names and gi numbers, respectively.
    33 </p>
    3423
    35 <p>Reference:</p>
    36 (1) Florea,L., Hartzell,G., Zhang,Z., Rubin,G.M. and Miller,W. (1998)
    37 <br>Computer program for aligning a cDNA sequence with a
    38 genomic DNA sequence. Genome Res., 8: 967.974.
    39 
    40 }}}
     24''Reference:''
     25 1. Florea,L., Hartzell,G., Zhang,Z., Rubin,G.M. and Miller,W. (1998) Computer program for aligning a cDNA sequence with a genomic DNA sequence. Genome Res., 8: 967.974.