Pragmatic Bioinformatics: Human Genome in 5 Minutes

A brief tutorial that illustrates how to download the uniprot protein database, extract the human proteome, and then analyze the sequences with the PDB solved 3D structure database. More at http://pragmaticbioinformatics.blogspot.org

Category:

Education

Tags:

• Pragmatic
• Bioinformatics
• Genome
• Proteome
• Human
• PDB
• Uniprot
• fasta_filter

[jungleman68]

I am majoring in this but I really have no idea what I will be doing. is linear algebra useful?

[curlyjunglejake]

@jungleman68 Probability and discrete math in general. From CS, you want to take as many algorithm classes as possible. From biology, I would recommend molecular biology, cell biology, immunology and population genetics. Get into the R analytical package as early as possible. Almost all of the academic code expects familiarity with unix command line. If I knew a little more about your specific interests in the field I might be able to be a bit more helpful.

[sammipooh]

Informative vid thanks. I'm wondering about your prog for filtering FASTA format files, I'm a follower of the BioPerl project and theres good modules in there for doing stuff like FASTA filtering.

I'm interested in what OS you're running on (what do you generally use for bioinformatics work)?

Its kinda fuzzy and can't really see all of your shell output and such.

Anyways, thanks.

[curlyjunglejake]

Hey Sammi,

Thanks for the comments. I do most of my work on Redhat or OSX. The example script I run in the video doesn't use bioperl, although I'm also a fan. If you are still interested in teh code let me know and I'll post it somewhere.

[jungleman68]

@curlyjunglejake oh god. I took linear algebra and differential equations and I'm planning on immunology but there is no way I can take everything. I'm actually majoring in Molecular Biology and Bioinformatics as a combined major so it may be different. I took Computer Science 1 and 2. Should I take more? that was all that was required. What's an R analytical package? If I come off as an idiot, it's because I haven't actually taken any bioinformatics classes yet. thank you.

[allenDGoon]

not impressed 

[MrBorsetti]

@sammipooh "I'm interested in what OS you're running on (what do you generally use for bioinformatics work)?"

Mostely with UNIX OS. A tip for using tools and other bio-informatic stuff: lern Python (google it up, also look up biopython.)

[nanobiotechpooja]

good work curly... :) pls post the code for FASTA format filters

[ebbie2009]

hey, that wasnt five minutes asshole. jk! : )

[c1zx]

I have no idea what you're talking about, however, the picture does look like DNA. And there does appear to be a computer program involved, but the rest sounds like someone mumbling something in the background.

[rmoradia]

nice work ... but could'nt see anything ...so of no use..... nothign to learn from it ..

[spyke4995]

?! wow