Exchanging lysines for arginines with increases in GC content: correlations!
Note: No guaranties whatsoever. If you want to try the exercise, I have the original table of genomes with their sizes and GC content at figshare. Click here to download … Continue reading
Exchanging lysines for arginines with increases in GC content: counts
Note: No guaranties whatsoever. If you want to try the exercise, I have the original table of genomes with their sizes and GC content at figshare. Click here to download … Continue reading
Exchanging lysines for arginines with increases in GC content: choosing a genome subset
Note: No guaranties whatsoever. If you want to try the exercise, I have the original table of genomes with their sizes and GC content at figshare. Click here to download … Continue reading
Exchanging lysines for arginines with increases in GC content: preparation
Note: No guaranties whatsoever. If you want to try the exercise, I have the original table of genomes with their sizes and GC content at figshare. Click here to download … Continue reading
Compiling NCBI’s blast 2.2.28+ in Mountain Lion
Note: left gutter and numbers in shell commands below to help differentiate the terminal commands and outputs from the text describing what I did. Recently, NCBI sent an e-mail about … Continue reading
Note on the perl programming example for newbies
Note: Not intended for professional programmers, but as example for non-programmers wishing to see some programming action. Also a disclaimer: No warranties whatsoever. In the little perl programming example for … Continue reading
Little PERL programming example for biology newbies
Note: Not intended for professional programmers, but as example for non-programmers wishing to see some programming action. Also a disclaimer: No warranties whatsoever. During an exercise in my intro course … Continue reading
And now BLAT 35 won’t compile in my Mountain Lion, or will it?
I just learned that the new version of the BLAST-like alignment tool, blat 35, was released last november. So, of course, I immediately downloaded and tried to compile it. Followed … Continue reading
If FTPing files from NCBI is too slow, they have rsync!
A quick tip. NCBI’s genomic files are not compressed, which translates into slow file transfer. However, the server can also be accessed via rsync, and the “-z” option in rsync … Continue reading
If ssearch36 gets stuck while comparing sequences in your mac
Quick note. When I was comparing the protein sequences from C. glomerans PW2 to those in E. coli K12 MG1655, the program would get stuck with this sequence: >gi|328954742|ref|YP_004372075.1| MSKTIPELTLDNFDLVMQSKLPVLVDFWAPWCGPCRTLSPIVEQVAEEMSERITVAKCNVDENQDLAMKYGVMS IPTLVLFRDGAEVSRTVGAMPKPKLVAEIEKNL … Continue reading
Publications
- Phylogenomic clustering for selecting non-redundant genomes for comparative genomics.
- Metagenomic annotation networks: construction and applications.
- The evolutionary dynamics of functional modules and the extraordinary plasticity of regulons: the Escherichia coli perspective.
- Bacterial biogeography of the human digestive tract.
- Open resource metagenomics: a model for sharing metagenomic libraries.
