Difference between revisions of "Two Eel Scaffolds"

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This is a small gene, however these alignments are not conclusive, though it is clear that eelScaffold32 has a higher probability of harbouring pdcd10b.
 
This is a small gene, however these alignments are not conclusive, though it is clear that eelScaffold32 has a higher probability of harbouring pdcd10b.
  
 +
 +
== nrd1a's 37 exons against eelScaffold32 ==
  
 
  SFI    ALEN    SCORE  IDEN    IPT    SIM    GAPS    GPT    TSC    TEC    PET    QSC    QEC    QLN    PEQ
 
  SFI    ALEN    SCORE  IDEN    IPT    SIM    GAPS    GPT    TSC    TEC    PET    QSC    QEC    QLN    PEQ
Line 100: Line 102:
 
  22      94      119.0  60      63.8    60      20      21.3    668713  668800  0.0    1      80      101    79.2
 
  22      94      119.0  60      63.8    60      20      21.3    668713  668800  0.0    1      80      101    79.2
 
  8      141    145.5  88      62.4    88      30      21.3    669021  669148  0.0    28      151    154    80.5
 
  8      141    145.5  88      62.4    88      30      21.3    669021  669148  0.0    28      151    154    80.5
  32      69      120.0  47      68.1    47      7      10.1    670437  670500  0.0    9      75      84      79.
+
  32      69      120.0  47      68.1    47      7      10.1    670437  670500  0.0    9      75      84      79.8

Revision as of 14:36, 13 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 (Oreochromis niloticus, Ensembl abbreviation ONI) to be the reference.

There are two genes expected to be around about the regions covered by these scaffolds:

  • eelScaffold32 contains any part of PDCD10b (Programmed cell death 10b).
  • eelScaffold320 contains any part of nrd1a (Nardilysin, N-arginine dibasic convertase)

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.

An example Augustus command line is as follows:

augustus --species=lamprey eelScaffold320.fa >aug_s320_lp.gtf

Augustus outputs in the GTF format, for visual browsing on JBrowse, we need to convert to the related format, GFF:

gtf2gff.pl --printExon --gff3 < aug_s32_lp.gtf --out=aug_s32_lp.gff

We are also probably interested in the CDS and proteins sequences of the predicted genes, we can use the follown Augustus-supplied script:

getAnnoFasta.pl --seqfile=eelScaffold32.fa aug_s32_lp.gtf

Detecting presence of pdcd10b and nrd1a

We take the exons of these genes and apply Waterstone alignment (via the Emboss program) with the scaffolds to them. We order via scaffold starting site.

pdcd10b's 7 exons against eelScaffold32

SFI     ALEN    SCORE   IDEN    IPT     SIM     GAPS    GPT     TSC     TEC     PET     QSC     QEC     QLN     PEQ
5       89      125.5   56      62.9    56      15      16.9    92493   92577   0.0     1       78      79      98.7
6       97      113.0   59      60.8    59      20      20.6    222386  222481  0.0     4       81      83      94.0
7       80      112.0   52      65.0    52      16      20.0    153839  153911  0.0     1       71      82      86.6
2       54      105.0   37      68.5    37      7       13.0    270271  270324  0.0     2       48      54      87.0
1       91      134.0   58      63.7    58      9       9.9     305491  305572  0.0     6       96      96      94.8
4       149     161.5   91      61.1    91      29      19.5    337277  337419  0.0     2       127     127     99.2
3       112     129.5   69      61.6    69      16      14.3    607211  607313  0.0     7       111     118     89.0
Total score for all alignments = 880.5

pdcd10b's 7 exons against eelScaffold320

SFI     ALEN    SCORE   IDEN    IPT     SIM     GAPS    GPT     TSC     TEC     PET     QSC     QEC     QLN     PEQ
5       51      105.0   36      70.6    36      5       9.8     13517   13567   0.0     27      72      79      58.2
1       110     130.0   70      63.6    70      25      22.7    52225   52323   0.0     1       96      96      100.0
6       89      116.5   55      61.8    55      15      16.9    60604   60688   0.0     6       83      83      94.0
2       50      97.0    36      72.0    36      7       14.0    64406   64450   0.0     1       48      54      88.9
7       84      112.5   55      65.5    55      14      16.7    162512  162589  0.0     7       82      82      92.7
4       124     138.5   79      63.7    79      19      15.3    222772  222891  0.0     18      126     127     85.8
3       79      131.0   54      68.4    54      9       11.4    238985  239059  0.0     24      97      118     62.7

pdcd10b discussion

This is a small gene, however these alignments are not conclusive, though it is clear that eelScaffold32 has a higher probability of harbouring pdcd10b.


nrd1a's 37 exons against eelScaffold32

SFI     ALEN    SCORE   IDEN    IPT     SIM     GAPS    GPT     TSC     TEC     PET     QSC     QEC     QLN     PEQ
2       270     217.5   160     59.3    160     60      22.2    4926    5175    0.0     34      263     324     71.0
3       235     257.0   143     60.9    143     35      14.9    9693    9920    0.0     5       211     241     85.9
15      88      117.5   54      61.4    54      14      15.9    66759   66843   0.0     2       78      78      98.7
12      34      104.0   28      82.4    28      2       5.9     67614   67647   0.0     24      55      58      55.2
36      73      114.5   47      64.4    47      14      19.2    140070  140139  0.0     3       64      70      88.6
4       37      104.0   28      75.7    28      0       0.0     159420  159456  0.0     2       38      38      97.4
23      18      72.0    16      88.9    16      0       0.0     190407  190424  0.0     5       22      22      81.8
33      108     115.5   66      61.1    66      24      22.2    214642  214747  0.0     5       90      91      94.5
19      108     133.5   69      63.9    69      13      12.0    222360  222458  0.0     1       104     105     99.0
13      84      109.5   52      61.9    52      15      17.9    237021  237101  0.0     3       74      74      97.3
17      60      97.5    41      68.3    41      14      23.3    258142  258195  0.0     2       53      59      88.1
35      98      124.0   60      61.2    60      19      19.4    259372  259461  0.0     1       87      90      96.7
29      126     162.0   79      62.7    79      20      15.9    268052  268173  0.0     6       115     139     79.1
18      46      105.5   34      73.9    34      4       8.7     281107  281152  0.0     1       42      55      76.4
10      107     125.5   69      64.5    69      20      18.7    342133  342236  0.0     6       95      96      93.8
21      94      131.0   60      63.8    60      18      19.1    365037  365120  0.0     1       86      87      98.9
20      136     131.0   82      60.3    82      28      20.6    380436  380559  0.0     2       121     124     96.8
34      127     131.0   78      61.4    78      28      22.0    387971  388090  0.0     1       106     117     90.6
25      140     154.0   86      61.4    86      20      14.3    409140  409267  0.0     9       140     151     87.4
37      125     149.5   78      62.4    78      30      24.0    411212  411315  0.0     15      130     131     88.5
9       77      113.5   50      64.9    50      11      14.3    478120  478193  0.0     4       72      74      93.2
1       609     297.5   343     56.3    343     143     23.5    491670  492216  0.1     4       531     541     97.6
16      120     147.0   72      60.0    72      11      9.2     519285  519397  0.0     2       117     121     95.9
28      35      76.0    25      71.4    25      4       11.4    522407  522440  0.0     1       32      32      100.0
26      124     147.5   76      61.3    76      28      22.6    531064  531176  0.0     21      127     128     83.6
31      55      108.5   40      72.7    40      9       16.4    540137  540190  0.0     3       49      53      88.7
14      73      107.0   50      68.5    50      16      21.9    557391  557458  0.0     3       64      70      88.6
6       23      67.0    18      78.3    18      3       13.0    571200  571222  0.0     3       22      23      87.0
11      144     144.0   86      59.7    86      34      23.6    586719  586853  0.0     3       121     123     96.7
30      50      95.5    35      70.0    35      7       14.0    599465  599511  0.0     3       48      48      95.8
7       54      105.0   38      70.4    38      6       11.1    599975  600025  0.0     30      80      82      62.2
5       21      72.0    18      85.7    18      1       4.8     604115  604135  0.0     5       24      26      76.9
27      173     176.5   105     60.7    105     39      22.5    621983  622127  0.0     2       163     163     99.4
24      46      98.0    34      73.9    34      4       8.7     655376  655420  0.0     6       48      52      82.7
22      94      119.0   60      63.8    60      20      21.3    668713  668800  0.0     1       80      101     79.2
8       141     145.5   88      62.4    88      30      21.3    669021  669148  0.0     28      151     154     80.5
32      69      120.0   47      68.1    47      7       10.1    670437  670500  0.0     9       75      84      79.8