{"id":202,"date":"2024-05-06T17:42:13","date_gmt":"2024-05-06T17:42:13","guid":{"rendered":"https:\/\/sites.wp.odu.edu\/awolter\/?post_type=portfolio&p=202"},"modified":"2024-05-06T17:42:13","modified_gmt":"2024-05-06T17:42:13","slug":"glimmer-command-line-analyzing-cds-locations","status":"publish","type":"portfolio","link":"https:\/\/sites.wp.odu.edu\/awolter\/portfolio\/glimmer-command-line-analyzing-cds-locations\/","title":{"rendered":"GLIMMER Command Line: Analyzing CDS Locations"},"content":{"rendered":"

Glimmer to analyze CDSs in a partial sequence<\/em><\/p>

For this example, I will use the Spiroplasma helicoides strain TABS-2, whose genome was submitted to GenBank on August 23, 2016.<\/p>

The first portion will require a training  file. This will be the whole genome of Spiroplasma helicoides strain TABS-2.<\/p>

This will enable the program to understand the genome and the way to deal with my data input and the required output. <\/p>

My second file contains the partial sequence with CDS locations . <\/p>

Training and determining determine CDS locations<\/em><\/strong> <\/em><\/strong><\/em><\/strong><\/p>

I have logged into the BFX server and uploaded the full and partial files so I can work with GLIMMER in terminal:<\/strong><\/p>

Below you can find a partial list of commands to retrieve the\u00a0orbs below. For more detailed information please see the work flow from terminal below:<\/strong><\/p>

Training Set:<\/p> 

full genome=> sheli.fasta   Prediction sequence:  partial genome => sheliprt.fasta     [awolter1@bfx3 ~]$ less sheliglimmer.predict  [awolter1@bfx3 ~]$ extract -t sheliprt.fasta sheliglimmer.predict > sheliprt.glimmer     >Spiroplasma helicoides strain TABS-2, partial sequence  [awolter1@bfx3 ~]$ ls  sheli.fasta           sheli.icm       sheliprt.glimmer  sheliglimmer.detail   sheli.longorfs  sheli.train  sheliglimmer.predict  sheliprt.fasta  xyz.icm  [awolter1@bfx3 ~]$ less sheliprt.glimmer  [awolter1@bfx3 ~]$ less sheliglimmer.predict     >Spiroplasma helicoides strain TABS-2, partial sequence  orf00001      635      991  +2     4.13  orf00002      998     1141  +2     4.42  orf00003     1154     1312  +2     2.30  orf00004     1334     1978  +2     5.68  orf00006     2242     2463  +1     6.25  orf00008     2585     4003  +2     8.80  orf00009     4010     4678  +2     8.48  orf00010     4880     5143  +2     6.98  <\/code><\/pre>    
<\/p>    
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<\/p>    
GLIMMER Session in Terminal<\/em><\/strong>:<\/p>    
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Glimmer to analyze CDSs in a partial sequence For this example, I will use the Spiroplasma helicoides strain TABS-2, whose genome was submitted to GenBank on August 23, 2016. The first portion will require a training  file. This will be the whole genome of Spiroplasma helicoides strain TABS-2. This will enable the program to understand the genome and the way to deal with […]<\/p>\n","protected":false},"author":28160,"featured_media":0,"menu_order":0,"comment_status":"open","ping_status":"closed","template":"","meta":{"wds_primary_portfolio-type":0},"portfolio-type":[],"_links":{"self":[{"href":"https:\/\/sites.wp.odu.edu\/awolter\/wp-json\/wp\/v2\/portfolio\/202"}],"collection":[{"href":"https:\/\/sites.wp.odu.edu\/awolter\/wp-json\/wp\/v2\/portfolio"}],"about":[{"href":"https:\/\/sites.wp.odu.edu\/awolter\/wp-json\/wp\/v2\/types\/portfolio"}],"author":[{"embeddable":true,"href":"https:\/\/sites.wp.odu.edu\/awolter\/wp-json\/wp\/v2\/users\/28160"}],"replies":[{"embeddable":true,"href":"https:\/\/sites.wp.odu.edu\/awolter\/wp-json\/wp\/v2\/comments?post=202"}],"wp:attachment":[{"href":"https:\/\/sites.wp.odu.edu\/awolter\/wp-json\/wp\/v2\/media?parent=202"}],"wp:term":[{"taxonomy":"portfolio-type","embeddable":true,"href":"https:\/\/sites.wp.odu.edu\/awolter\/wp-json\/wp\/v2\/portfolio-type?post=202"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}