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 my data input and the required output. 

My second file contains the partial sequence with CDS locations . 

Training and determining determine CDS locations 

I have logged into the BFX server and uploaded the full and partial files so I can work with GLIMMER in terminal:

Below you can find a partial list of commands to retrieve the orbs below. For more detailed information please see the work flow from terminal below:

Training Set:

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  

GLIMMER Session in Terminal: