Difference between revisions of "Two Eel Scaffolds"

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  getAnnoFasta.pl --seqfile=eelScaffold32.fa aug_s32_lp.gtf
 
  getAnnoFasta.pl --seqfile=eelScaffold32.fa aug_s32_lp.gtf
 +
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In order to visually navigate the results of these annotations, they can be viewed on a browser [http://stab.st-andrews.ac.uk/JBrowse-1.12.1 here].
  
 
= Detecting presence of '''pdcd10b''' and '''nrd1a''' =
 
= 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.
+
We take the exons of these genes and apply Smith-Waterman alignment (via the Emboss program) with the scaffolds to them. We order via scaffold starting site.
  
 
== pdcd10b's 7 exons against eelScaffold32 ==
 
== pdcd10b's 7 exons against eelScaffold32 ==

Revision as of 15:38, 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

In order to visually navigate the results of these annotations, they can be viewed on a browser here.

Detecting presence of pdcd10b and nrd1a

We take the exons of these genes and apply Smith-Waterman 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
Score for 7 query sequences (total 639 bp) against target (679422 bp) = 880.50

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
Score for 7 query sequences (total 639 bp) against target (246433 bp) = 830.5

pdcd10b discussion

This is a small gene, however we cannot say these alignments are conclusive. It is clear however 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
Score for 37 query sequences (total 4025 bp) against target (679422 bp) = 4795.50

nrd1a's 7 exons against eelScaffold320

SFI     ALEN    SCORE   IDEN    IPT     SIM     GAPS    GPT     TSC     TEC     PET     QSC     QEC     QLN     PEQ
32      52      99.5    36      69.2    36      4       7.7     11214   11261   0.0     10      61      84      61.9
18      46      105.5   34      73.9    34      4       8.7     21678   21720   0.0     1       45      55      81.8
17      70      95.0    45      64.3    45      20      28.6    22625   22693   0.0     3       53      59      86.4
24      40      96.5    29      72.5    29      2       5.0     22849   22886   0.0     8       47      52      76.9
23      21      69.0    17      81.0    17      0       0.0     26374   26394   0.0     1       21      22      95.5
6       18      72.0    16      88.9    16      0       0.0     28762   28779   0.0     5       22      23      78.3
14      64      105.5   42      65.6    42      9       14.1    42560   42621   0.0     12      68      70      81.4
2       315     228.0   183     58.1    183     64      20.3    46282   46552   0.1     7       301     324     91.0
21      90      112.5   58      64.4    58      17      18.9    80763   80842   0.0     3       85      87      95.4
25      153     138.0   88      57.5    88      27      17.6    81195   81324   0.1     1       149     151     98.7
11      81      148.5   55      67.9    55      10      12.3    81550   81625   0.0     47      122     123     61.8
1       525     261.0   294     56.0    294     105     20.0    83281   83764   0.2     2       462     541     85.2
15      61      107.0   40      65.6    40      4       6.6     89643   89699   0.0     8       68      78      78.2
28      39      78.0    28      71.8    28      8       20.5    92398   92435   0.0     1       32      32      100.0
8       168     147.0   104     61.9    104     32      19.0    97584   97741   0.1     8       153     154     94.8
3       254     229.0   150     59.1    150     55      21.7    106270  106501  0.1     6       226     241     91.7
31      54      88.5    37      68.5    37      6       11.1    106293  106342  0.0     2       53      53      98.1
29      129     142.5   79      61.2    79      30      23.3    107213  107332  0.0     23      130     139     77.7
13      70      119.0   46      65.7    46      5       7.1     108538  108605  0.0     1       67      74      90.5
4       37      84.5    27      73.0    27      3       8.1     129499  129534  0.0     3       37      38      92.1
37      131     128.5   79      60.3    79      26      19.8    133637  133753  0.0     13      131     131     90.8
35      96      114.5   60      62.5    60      21      21.9    135814  135897  0.0     1       87      90      96.7
9       78      106.5   50      64.1    50      14      17.9    136915  136989  0.0     5       71      74      90.5
30      39      87.0    27      69.2    27      0       0.0     137258  137296  0.0     1       39      48      81.2
22      114     120.0   69      60.5    69      20      17.5    143789  143896  0.0     2       101     101     99.0
5       30      64.5    22      73.3    22      6       20.0    158927  158955  0.0     1       25      26      96.2
27      176     145.0   102     58.0    102     39      22.2    161163  161325  0.1     13      162     163     92.0
33      89      109.0   56      62.9    56      19      21.3    164489  164570  0.0     5       81      91      84.6
10      82      119.0   52      63.4    52      11      13.4    168702  168776  0.0     1       78      96      81.2
7       81      106.5   50      61.7    50      7       8.6     178661  178740  0.0     4       78      82      91.5
20      121     141.5   76      62.8    76      21      17.4    178727  178838  0.0     14      122     124     87.9
12      43      98.0    31      72.1    31      4       9.3     202832  202872  0.0     5       45      58      70.7
36      65      118.0   44      67.7    44      8       12.3    208219  208279  0.0     3       63      70      87.1
19      120     157.5   76      63.3    76      29      24.2    221343  221456  0.0     2       98      105     92.4
34      86      124.0   58      67.4    58      14      16.3    221411  221484  0.0     19      102     117     71.8
26      123     127.5   74      60.2    74      14      11.4    225229  225348  0.0     4       115     128     87.5
16      129     126.0   77      59.7    77      21      16.3    226946  227071  0.1     11      121     121     91.7
Score for 37 query sequences (total 4025 bp) against target (246433 bp) = 4519.50

nrd1a discussion

Also an inconclusive analysis. EelScaffold32 again is more likely to be harbouring this second gene. Being some three time longer, it has a higher prior likelihood for this.