# My Favorite Gene
## DNMT

This page was created by Steven Roberts - [@sr320](https://github.com/sr320)



**Is it in the Geoduck transcriptome?**

---

The first thing I did was get a sequence from Genbank in a species with fully annotated genome.

[Here is a movie](http://owl.fish.washington.edu/btea/movies/Steven-serarches-for-DNMT.mov) of me doing just that! 

This is a screenshot of the NCBI page

<img src="http://eagle.fish.washington.edu/cnidarian/skitch/PREDICTED__Homo_sapiens_DNA__cytosine-5-_-methyltransferase_1__DNMT1___-_Nucleotide_-_NCBI_1BD976CD.png"/ width = 50%>



---

This is a direct link to the page
<http://www.ncbi.nlm.nih.gov/nuccore/768001213>


##Blasting against Geoduck database
![picture of Geoduck](https://www.evernote.com/l/AAr8G9VTSV1HVpsXRF1D65N1DR2gFiQ1AKMB/image.png)


![picture of Geoduck](../img/pic-geoduck.png)

### Brent Dissecting Tissue used for making RNA-seq Libraries
<iframe width="560" height="315" src="https://www.youtube.com/embed/Acj3ta5UqR0?rel=0" frameborder="0" allowfullscreen></iframe>


my code :)

```bash
!blastn \
-query /Users/sr320/git-repos/course-btea/data/Hsapien_DNMT.fasta \
-db /Users/sr320/Desktop/big-data/db/Geo_Female \
-task blastn \
-outfmt 6 \
-out /Users/sr320/Desktop/big-data/DNMT_blastn_GeoFemale.out
```

When I run that I found a MATCH!!

Here is the top hit for GeoDuck Female

```
gi|768001213|ref|XM_011527774.1|	Geo_Pool_F_GGCTAC_L006_R1_001_val_1_(paired)_contig_23384	70.89	962	258	9	3846	4802	1744	800	1e-125	 452
```

Here is the top hit for GeoDuck Male

```
gi|768001213|ref|XM_011527774.1|	Geo_Pool_M_CTTGTA_L006_R1_001_val_1_(paired)_contig_7892	70.52	1472	394	14	3339	4802	2334	3773	0.0	 672
```


Here is the top hit for the Oly Male library

```
gi|768001213|ref|XM_011527774.1|	filtered_106A_Male_Mix_TAGCTT_L004_R1_(paired)_contig_9003	69.95	1764	476	15	3071	4801	2838	4580	0.0	 773
```


Here is the top hit for the Oly Female library

```
gi|768001213|ref|XM_011527774.1|	filtered_108A_Female_Mix_GGCTAC_L004_R1_(paired)_contig_8192	70.01	1764	475	15	3071	4801	2775	4517	0.0	 778
```


#Results Table

Library |  Sequence Name | evalue
---------|-------------|---------
Oly Male | contig_9003 | 0.0	
Oly Female | contig_8192 | 0.0
Geo Male | contig_7892 | 0.0
Geo Female | contig_23384 | 1e-125