George Heller

3/28/17

Individual Project:

I came to class to find that Yanni and Skylar joined the group. Braden explained to me that we would have to flesh out our plan hastily. He had talked to Dr. Adair, who had told him that our idea would not work. Our group needed an idea. We liked the idea of a phylogenetic tree, so I spent the day researching articles on them.

Braden and I decided to meet after class to have an idea before next class. I’m sure Yanni and Skylar did something.

I was too sick to make it to class.

George Heller

3/14/17

Final Project:

Group: Braden

We discussed an idea for our group project: Use bioinformatics tools to guess the functions of hypothetical proteins, especially by comparing similar protein groups, or phams, where some are defined and others are not.

Independent annotations of Timinator:

Today we continued annotating the phage Timinator. My assigned genes are 8*, 30*, 52, 74, and 47.

*Finished prior to class

The annotations are to be done as before: using NCBI, Phagesdb, DNAMaster, GeneMark, phamer and starterator, and HHPred.

Gene 8 (DNA Master format):

Start: 7141bp Stop: 7527bp FWD GAP: 38bp Gap SD Final Value: SD Score: -2.137 (Best score) Z-Value: 3.401 CP: The gene is covered SCS: Agrees with Glimmer, Agrees with GeneMark NCBI BLAST: hypothetical protein BARRETLEMON_8 [Arthrobacter phage BarretLemon] E-Value: 0.0 CDD: No good hit PhagesDB BLAST: StevieBAY_Draft_8, function unknown, 128 Q1 S1 E-Value: 7e-69 HHPred: No good hit LO: Yes ST: Agrees with Starterator F: NKF FS: HHPred, NCBI Notes: No hit, but this seems plausible: (3gqh_A Preneck appendage protein; beta barrel, viral protein; 1.80A {Bacillus phage PHI29} E .00068 Prob 97.90) Pham:6421

Gene 30:

Start: 25730bp Stop: 26065bp FWD GAP: 43bp Gap SD Final Value: SD Score: -4.891 (Best score) Z-Value: 2.412 CP: The gene is covered SCS: Agrees with Glimmer, Agrees with GeneMark NCBI BLAST: tail lysozyme [Arthrobacter phage BarretLemon] Q:1 S:1 E-Value: 2e-73 CDD: GPW_gp25 Superfamily E-Value: 1.93 e-4 PhagesDB BLAST: BarretLemon_30, tail lysozyme, 111 224 2e-59 Q1 S1 E-Value: 2e-59 HHPred: 2ia7_A Tail lysozyme, putative; NP_952040.1, putative tail lysozyme, structural genomics, JO center for
structural genomics, JCSG; 1.44A {Geobacter sulfurreducens} E-Value: 3.3e-24 LO: Yes ST: F: NKF FS: Gene 25-like Tail Lysozyme HHPred, NCBI Notes: Pham:7938

Gene 74 (reverse):

Start: 48075bp Stop: 46807bp BKWD GAP: 79bp Gap SD Final Value: SD Score: -2.354 (Best score) Z-Value: CP: The gene is covered SCS: Disagrees with Glimmer, Disagrees with GeneMark NCBI BLAST: BarretLemon_74, function unknown, 214 E-Value: 0.0 CDD: Beta_Clamp E-Value: 3 e-43 PhagesDB BLAST: No good hit HHPred: No good hit LO: No better sd score ST: F: FS: Notes:

Conclusion:

Today was another slow day, but I should be finished by next class. I spent the majority of the class working on annotating a reverse gene. I spent more time than I would like to admit being confused because I was getting the numbers mixed up.

George Heller

2/28/17

Independent annotating:

Today we began annotating the phage Timinator. My assigned genes were 8, 30, 52, 74, and 47. I did not get much done today as I had a severe migraine.

The annotations were done as before: using NCBI, Phagesdb, DNAMaster, GeneMark, phamer and starterator, and HHPred.

Gene 8 (DNA Master format):

Start: 7141bp Stop: 7527bp FWD GAP: 38bp Gap SD Final Value: SD Score: -2.137 (Best score) Z-Value: 3.401 CP: The gene is covered SCS: Agrees with Glimmer, Agrees with GeneMark NCBI BLAST: hypothetical protein BARRETLEMON_8 [Arthrobacter phage BarretLemon] E-Value: 0.0 CDD: No good hit PhagesDB BLAST: StevieBAY_Draft_8, function unknown, 128 Q1 S1 E-Value: 7e-69 HHPred: No good hit LO: Yes ST: Agrees with Starterator F: NKF FS: HHPred, NCBI Notes: No hit, but this seems plausible: (3gqh_A Preneck appendage protein; beta barrel, viral protein; 1.80A {Bacillus phage PHI29} E .00068 Prob 97.90) Pham:6421

Gene 30:

Start: 25730bp Stop: 26065bp FWD GAP: 43bp Gap SD Final Value: SD Score: -4.891 (Best score) Z-Value: 2.412 CP: The gene is covered SCS: Agrees with Glimmer, Agrees with GeneMark NCBI BLAST: tail lysozyme [Arthrobacter phage BarretLemon] Q:1 S:1 E-Value: 2e-73 CDD: GPW_gp25 Superfamily E-Value: 1.93 e-4 PhagesDB BLAST: BarretLemon_30, tail lysozyme, 111 224 2e-59 Q1 S1 E-Value: 2e-59 HHPred: 2ia7_A Tail lysozyme, putative; NP_952040.1, putative tail lysozyme, structural genomics, JO center for
structural genomics, JCSG; 1.44A {Geobacter sulfurreducens} E-Value: 3.3e-24 LO: Yes ST: F: NKF FS: Gene 25-like Tail Lysozyme HHPred, NCBI Notes: Pham:7938

Conclusion:

Today was a slow day and I was not feeling well. I did not get much done, but I do not anticipate any difficulty with these annotations.

George Heller

2/21/17

Presentations: Today we made our presentations in preparation for completing Lore annotations. We finished our presentation in the first part of class then presented.

We made some changes to the Lore genome; Gene twenty-one was deleted in its entirety and some genes need to be re-evaluated because of errors in their annotations.  Once the corrections are made, we will be able to finalize the genome.

George Heller

2/14/17

Group: George, Braden

Range: 7000-8400 with genes 12 and 13

More Lore! We had finished annotating our section, so Lathan suggested that we double-check gene 13, the gene we shared with another group.

Presentation: We began making a power point presentation to showcase our group’s annotations.

Gene 13:  We made a new row at the bottom of the google sheet and went through annotating gene thirteen to make sure that it was done right the first time, which it was. Our results:

7279bp Stop: 9276bp FWD GAP: 110bp Gap SD Final Value: SD Score: -4.389 (2nd best score) Gap was too huge for best, Starterator calls 7279 Z-Value: 2.209 CP: The gene is covered SCS: Agrees with Glimmer, Agrees with GeneMark NCBI BLAST: Tapemeasure protein Arthrobacterphage Toulouse E-Value: 0.0 CDD: Phage-related protein [Mobilome: prophages, transposons] E-Value: 5.90e-11 PhagesDB BLAST: StewieGriff_Draft_13, function unknown, 665 E-Value: 0.0 HHPred: No good hit LO: Yes ST: Agrees with Starterator F: tape measure protein FS: NCBI Notes:

To conclude, we have really gotten our annotation process down. we have finished annotating lore and will be making our power point over the weekend.

George Heller

2/7/17

Starterator: the sister-program to Phamerator allows us to use the gene Pham numbers from phamerator in order to see where most other phage’s start sites were. Starterator runs similarly to phamerator.

Group: George, Braden Range:

Range: 7000-8400

Full Annotation: Today, we had been given the tools we need, we began annotating the phage Lore.  We had two genes in our range, 12 and 13, but took over gene 12 and passed gene 13 along to the next group, who had no gene of their own. Our gene was pretty simple, DNA Master had gotten a lot right. Our annotations:

Start: 6818bp Stop: 7168bp FWD GAP: 5bp Gap SD Final Value: SD Score: -2.761 (Best score) Z-Value: 3.342 CP: The gene is covered SCS: Agrees with Glimmer, Agrees with GeneMark NCBI BLAST: Hypothetical protein Arthrobacterphage Jessica q:1 s:1 E-Value: 3e-77 CDD: No good hit PhagesDB BLAST: StewieGriff_Draft_12, function unknown, 116 q:1 s:1 E-Value: 6e-62 HHPred: No good hit LO: Yes ST: Agrees with Starterator F: NKF FS: HHPred, NCBI, Phagesdb Notes: pham 4453

To conclude, I am enjoying annotations much more than I thought I would at the beginning of the semester. It is less about confirming whether or not a computer was right and following a mind-numbing procedure than it is about finding and synthesizing information we gather from several sources, including NCBI and HHPred.

George Heller

1/31/17

Phamerator, a program that will allow us to compare genomes grouped together in “Phams”.

Procedure: Today we began using Phamerator, a piece of software written for Linux in python. To open Phamerator, create a virtual machine, even though we are already running DNA Master in parallel, using Virtual Box. Log into the student account on the Phamerator box and open the program. Open the program’s phage tab and search for the phage you want.  Select the phage from the list or batch select multiple phages and hit the map button in the upper left. The graphical output is useful for comparing genomes and genes and can be used later on for programs like Starterator.

To conclude, Phamerator will be very useful but I am still confused by the convoluted way all of these programs are set up. Phamerator will let us see how genes fit together in organisms that are closely related to the ones we will be annotating and give us insight into how our genomes should come together.

George Heller

1/24/17

To become accustomed to using BLAST and learn to annotate:

Procedure:

From PhagesDB, Download Link.fasta,

Open DNAMaster, Auto Annotate,

Open Frames, Features,

Upload to GeneMark, Download PDF,

Fill out the notes for genes 2-5 and post

Take the amino acid sequence from the products tab, upload to BlastP

The closest match is the one with the least E-Value`

To Conclude, 

DNA Master is difficult to use, but annotating seems very straightforward.

George Heller

1/27/17

DNA Master

To acquaint ourselves with DNA master, the program we will be using for annotating, we calibrated WINE, calibrated DNA master itself, and then practiced using the auto-annotate feature.

Procedure:

Adjust DNA Master to archive to the desktop,

Set the color scheme,

Insert the Template,

Adjust to Karlin Medium, Kibbler 7,

Download and annotate Amigo.fasta

To conclude,

It is difficult to use OSX, It is odd that a computer that can natively run .NET on Windows must boot to OSX and use a WINE framework session to run a program, It is also an odd thing to run Unix-based programs on a virtual Linux machine instead of natively on OSX.