Difference between revisions of "Casey Dunn"

From MolEvol
(Exercise cheat sheet)
Line 1: Line 1:
 
[[File:Dunn.jpg|thumb|right]]
 
[[File:Dunn.jpg|thumb|right]]
 
=== Duration of Stay ===
 
=== Duration of Stay ===
I will arrive  July 23, and leave early on July 28.
+
 
  
 
=== Web pages ===
 
=== Web pages ===
Line 17: Line 17:
  
 
=== Lecture Materials ===
 
=== Lecture Materials ===
 +
 +
2013:
 
[http://www.brown.edu/Faculty/Dunn_Lab/Dunn_2013_mbl_s.pdf lecture slides]
 
[http://www.brown.edu/Faculty/Dunn_Lab/Dunn_2013_mbl_s.pdf lecture slides]
  

Revision as of 10:55, 28 July 2014

Dunn.jpg

Duration of Stay

Web pages

Lab - http://www.brown.edu/Faculty/Dunn_Lab/

CreatureCast - http://creaturecast.org/

Practical Computing for Biologists - http://practicalcomputing.org/

Code - https://bitbucket.org/caseywdunn

Twitter - @caseywdunn


Lecture Materials

2013: lecture slides


Here are links for some of the sites I talk about in the lecture:

Agalma transcriptome analysis tool

Agalma preprint

Agalma sample analysis

CreatureCast

Interactive tree



Below are some quick-references that I hope will be useful for the course:

Statistics

Computing


I'll be doing some exercises in class from the book I wrote with Steve Haddock, Practical Computing for Biologists. To follow along, you will need to have a text editor that supports regular expressions (sometimes called grep). Recommended editors include:

TextWrangler for OS X

JEdit for Linux and Windows (Requires that a Java runtime environment also be installed)

NotePad++ for Windows


Exercise cheat sheet

Text for examples in class:

Replace genus name with first letter and then a .

Agalma elegans

Frillagalma vitiazi

Cordagalma tottoni

Shortia galacifolia

Mus musculus



Remove tick and subsequent letter directions

+40 46'N +014 15'E

+21 17'N -157 52'W


Keep just the numbers, get rid of the letters 5th

3rd

2nd

4th



Exercise 1:

Copy and paste the following fasta file to your text editor:


>CAA58790.1= green fluorescent protein [Aequorea victoria]

MSKGEELFTGVVPILVELDGDVNGQKFSVRGEGEGDATYGKLTLKFICTTGKLPVPWPTLVTTFSYGVQCFSRYPDHMKQHDFLKSAMPEGYVQERTIFYKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKMEYNYNSHNVYIMGDKPKNGIKVNFKIRHNIKDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSALSQDPHGKRDHMVLLEFVTSAGITHGMDELYK

>AAZ67342.1= GFP-like red fluorescent protein [Corynactis californica]

MSLSKQVLPRDVKMRYHMDGCVNGHQFIIEGEGTGKPYEGKKILELRVTKGGPLPFAFDILSSVFTYGNRCFCEYPEDMPDYFKQSLPEGHSWERTLMFEDGGCGTASAHISLDKNCFVHKSTFHGVNFPANGPVMQKKTLNWEPSSELITAGDGILKGDVTMFLMLEGGHRLKCQFTTSYKAKKAVKMPPNHIIEHRLVRKEVADAVQIQEHAVAKHFIV

>ACX47247.1= green fluorescent protein [Haeckelia beehleri]

MEFEPEFFNKPVPLEMTLRGCVNGKEFMIFGKGEGDASKGNIKGKWILSHSEDGKCPMSWAVLAPTFAYGFKVFAKYPKDFAHFWQDCMPVGYSERRITRFGRLSGNDDIEQEGIMNTYHEVQMRERMVGDEITWIVESRVKLDATINENSPILMNDGLSEYRPNLERTVSFEDGLKNYSQFFYPIKDCETKDYIIANQMTHERPLSKCNKPGRLPPSHFKRTDLEQWKDSKEDKDHIVQEEITAFLLQAQDKDLQSLGIGM

>ABC68474.1= red fluorescent protein [Discosoma sp. RC-2004]

MRSSKNVIKEFMRFKVRMEGTVNGHEFEIEGEGEGRPYEGHNTVKLKVTKGGPLPFAWDILSPQFQYGSKVYVKHPADIPDYKKLSFPEGFKWERVMNFEDGGVVTVTQDPSLQDGCFIYKVKFIGVNFPSDGPVMQKKTMGWEASTERLYPRDGVLKGEIHKALKLKDGGHYLVEFKTIYMAKKPVQLPGYYYVDSKLDITSHNKDYTIVEQYERTEGRHHLFLKAELGSNVGER

>AAQ01183.1= green fluorescent protein 1 [Pontellina plumata]

MPAMKIECRISGTLNGVVFELVGGGEGIPEQGRMTNKMKSTKGALTFSPYLLSHVMGYGFYHFGTYPSGYENPFLHAANNGGYTNTRIEKYEDGGVLHVSFSYRYEAGRVIGDFKVVGTGFPEDSVIFTDKIIRSNATVEHLHPMGDNVLVGSFARTFSLRDGGYYSFVVDSHMHFKSAIHPSILQNGGSMFAFRRVEELHSNTELGIVEYQHAFKTPTAFA


Use your new regular expressions skills to convert the headers from the format: >CAA58790.1= GFP [Aequorea victoria] To: >CAA58790_Aequorea

Exercise 2:

Copy and paste this tree into your text editor:

((raccoon:19.19959,bear:6.80041):0.84600,((sea_lion:11.99700, seal:12.00300):7.52973,((monkey:100.85930,cat:47.14069):20.59201, weasel:18.87953):2.09460):3.87382,dog:25.46154);


Use regular expressions to remove the branch lengths.

Once you've done that, paste the tree into your editor again and truncate the branch lengths so that there are only two numbers after each decimal point.