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2 <& "/page/page_title.mas", title => "SGN: Frequently Asked Questions (FAQ)" &>
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12 This page contains questions that SGN users ask and
13 are useful to the larger SGN user community. Please
14 <a href="/contact/form">let
15 us know</a> if you have a question that you think
16 should be added.
18 <p><strong>Question:</strong> Where can I order clones?<br />
19 <strong>Answer:</strong> This depends on the species and on
20 the specific library. For tomato clones, you can
21 use the clone ordering facility at the <a href=
22 "http://ted.bti.cornell.edu/order/">Boyce Thompson
23 Institute</a>. For potato clones that were
24 sequenced as part of the U.S. potato genome
25 project, the ordering is handled by the <a href=
26 "http://genome.arizona.edu/orders/">Arizona Genome
27 Institute</a>. For all other libraries, please
28 contact the library submitters given on the library
29 detail pages (use the <a href=
30 "/search/direct_search.pl?search=ESTs">Library
31 Search</a> page to find the library in
32 question).</p>
34 <p><strong>Question:</strong> The SGN pages look really
35 messed up on my browser.<br />
36 <strong>Answer:</strong> You are working with an old browser
37 that does not support style sheets, such as the
38 browsers of the Netscape 4.x series. SGN pages
39 require style sheets and javascript to be turned
40 on.</p>
42 <p><strong>Question:</strong> Can I submit my data to
43 SGN?<br />
44 <strong>Answer:</strong> Please send us a message using the <a href=
45 "/contact/form">contact form</a>
46 with a description of the data you would like to
47 submit. We will then work with you to integrate
48 your data into the database and/or add it to the
49 FTP server.<br />
50 </p>
51 <p><strong>Question:</strong> Tomato genome has 12 chromosomes. However, some sequences are mapped to 'ch00'. What is 'ch00'? <br />
52 <strong>Answer:</strong> ch00 is a place holder for tomato sequences that could not be mapped to any of the 12 tomato chromosomes.
53 <br />
54 <p><strong>Question:</strong> What does the color gradient in the Gbrowse tracks mean? <br />
55 <strong>Answer:</strong> The intensity of the color signifies the degree of match between the feature and the genome sequence, the white color signifies the lowest match whereas the darkest color signifies the strongest match. You can find more detailed explanation by following the '?' button on the track of your interest.
57 <p>
58 <strong>Question:</strong> What do the identifiers of the format Solyc01g001010.1.1 mean?<br />
59 <strong>Answer:</strong> These identifiers denote loci, predicted mRNA and protein sequences from the tomato genome sequencing project. "Solyc" is the 5 letter abbreviation of <i>Solanum lycopersicum</i>, the 2 digit number following the 'Solyc' denotes the chromosome, 'g' denotes that the sequence is a gene, and the 6 digit number following the 'g' identifies the gene on the chromosome, starting at the top and counting in 10 increments. The first '.1' denotes the annotation version number of the locus (and if only the first number is given, denotes the locus), whereas the second '.1' denotes the transcript (a locus can give rise to many transcripts, splice variants), and also the proteins derived from these transcripts.
60 <br />
61 </p>
62 <p>
63 <strong>Question:</strong>How can I use the SGN Intron Finder tool for a batch of sequences?<br />
64 <strong>Answer:</strong> (1) You can enter multiple sequences to the <a href="/tools/intron_detection/find_introns.pl">form</a>. (2) If you are doing the blasting locally, try using the code below:<br/> <a href="https://github.com/solgenomics/sgn/blob/master/cgi-bin/tools/intron_detection/intron_finder_homology.pl"> code 1</a>, <a href="https://github.com/solgenomics/sgn/blob/master/lib/SGN/IntronFinder/Homology.pm">code 2</a>.
65 <br />
66 </p>
67 <p>
68 <strong>Question:</strong>What cultivar was used for the international tomato genome sequencing project ?<br />
69 <strong>Answer:</strong> <a href="/stock/676/view">Heinz 1706</a>.
70 <br />
71 </p>
72 <p>
73 <strong>Question:</strong> How can I download annotation features on the tomato genome?<br />
74 <strong>Answer:</strong> As an alternative to Gbrowse's download function, you can use this <a href="/search/features">tool</a> to select your region of interest and download the features using the download options at the top right of the page.
75 <br />
76 </p>
77 <p>
78 <strong>Question:</strong> How can I convert tomato unigene ids between builds?<br />
79 <strong>Answer: </strong>Use this <a href="ftp://ftp.solgenomics.net/unigene_builds/combined_species_assemblies/tomato_species/tomato_species_unigenes.v1.global_versionmapping.tab">file</a>, and read this <a href="ftp://ftp.solgenomics.net/unigene_builds/combined_species_assemblies/tomato_species/README_about_global_version_mapping.txt">key</a>. <b>Caveat</b>: a unigene may be split or merged with other unigene(s) in different builds. For unigenes of non-tomato species, look for similarly named files higher up in the ftp directory.
80 <br />
81 </p>
82 <p>
83 <strong>Question:</strong> How can I map tomato gene model ids (ITAG_2.3 annotation) to their corresponding SGN unigene ids (unigine build #2)?<br />
84 <strong>Answer: </strong>Use this <a href="ftp://ftp.solgenomics.net/unigene_builds/combined_species_assemblies/tomato_species/unigene_annotations/tomato_species_unigenes.v2.Solyc_ITAG2.3.genemodels.map.txt">file</a>, and read this <a href="ftp://ftp.solgenomics.net/unigene_builds/combined_species_assemblies/tomato_species/README_about_global_version_mapping.txt">note</a>.
85 <br />
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