Difference between revisions of "Two Eel Scaffolds"

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(Created page with "= Introduction = Two DNA scaffolds are presented: # '''eelScaffold32'''. 679 422 bp and 42.25% GC. # '''eelScaffold320'''. 246 433 bp and 43.47% GC. In terms special geens o...")
 
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# '''eelScaffold320'''. 246 433 bp and 43.47% GC.
 
# '''eelScaffold320'''. 246 433 bp and 43.47% GC.
  
In terms special geens of interest, it will be interesting to find out whether  
+
We take ''tilapia'' to be the
* '''eelScaffold32''' contains any part of PDCD10b.
+
 
* '''eelScaffold320''' contains any part of NRd1a.
+
In terms special genes of interest, it will be interesting to find out whether  
 +
* '''eelScaffold32''' contains any part of [http://www.ensembl.org/Oreochromis_niloticus/Gene/Summary?g=ENSONIG00000001157&db=core PDCD10b] (Programmed cell death 10b).
 +
* '''eelScaffold320''' contains any part of NRd1a  
  
 
= ORF Analysis =
 
= ORF Analysis =
  
ORF scan for sequences over 100 kbp usually throw up too much data, but it may happen
+
ORF scans for sequences over 100 kbp often throw up too much data, but it can be useful first step to see the complexity of the sequence.
 
 
 
 
  
 
= Gene Predictor =
 
= Gene Predictor =
  
 
One of the most up-to-date (2016) gene predictors is Augustus. It uses HMM profiles based on a related organism. In terms of eel, there are two given organisms: Zebra fish ('''zb''') and Lamprey
 
One of the most up-to-date (2016) gene predictors is Augustus. It uses HMM profiles based on a related organism. In terms of eel, there are two given organisms: Zebra fish ('''zb''') and Lamprey
('''lp''').
+
('''lp''') which Augustus makes available. Though tilapia is not available, it is possible - given time - to train and establish HMM profile for this organism.
  
 
The Augustus
 
The Augustus

Revision as of 14:21, 12 May 2016

Introduction

Two DNA scaffolds are presented:

  1. eelScaffold32. 679 422 bp and 42.25% GC.
  2. eelScaffold320. 246 433 bp and 43.47% GC.

We take tilapia to be the

In terms special genes of interest, it will be interesting to find out whether

  • eelScaffold32 contains any part of PDCD10b (Programmed cell death 10b).
  • eelScaffold320 contains any part of NRd1a

ORF Analysis

ORF scans for sequences over 100 kbp often throw up too much data, but it can be useful first step to see the complexity of the sequence.

Gene Predictor

One of the most up-to-date (2016) gene predictors is Augustus. It uses HMM profiles based on a related organism. In terms of eel, there are two given organisms: Zebra fish (zb) and Lamprey (lp) which Augustus makes available. Though tilapia is not available, it is possible - given time - to train and establish HMM profile for this organism.

The Augustus