n0b3l1a

Sunday, October 31, 2010

Alignment

*Free shift (or semi-global) alignments will ignore gaps at the beginning and end of the sequence, while Global alignments try to consider all positions.
Use Free shift alignments when some of the sequences are terminally truncated. Local alignments (such as BLAST) are useful for
finding short stretches of homology and are useful for finding sequence overlap or detecting a short internal sequence stretches that
are shared.

http://www.uoguelph.ca/plant/depttools/dnaanalysis.htm
www.cs.ecu.edu/hochberg/spring2006/LocalAlign.pdf
birg.cs.wright.edu/text/Ch2.ppt

Friday, October 29, 2010

Thursday, October 28, 2010

ncRNA non-coding RNA review papers

1: Galasso M, Elena Sana M, Volinia S. Non-coding RNAs: a key to future
personalized molecular therapy? Genome Med. 2010 Feb 18;2(2):12. PubMed PMID: 20236487; PubMed Central PMCID: PMC2847703.
http://www.ncbi.nlm.nih.gov/pubmed/20236487

1: Harrison BR, Yazgan O, Krebs JE. Life without RNAi: noncoding RNAs and their functions in Saccharomyces cerevisiae. Biochem Cell Biol. 2009 Oct;87(5):767-79. Review. PubMed PMID: 19898526.
http://www.ncbi.nlm.nih.gov/pubmed/19898526

1: Fabbri M, Calin GA. Beyond genomics: interpreting the 93% of the human genome that does not encode proteins. Curr Opin Drug Discov Devel. 2010 May;13(3):350-8. Review. PubMed PMID: 20443168.
http://www.ncbi.nlm.nih.gov/pubmed/20443168

1: Majer A, Booth SA. Computational methodologies for studying non-coding RNAs relevant to central nervous system function and dysfunction. Brain Res. 2010 Jun 18;1338:131-45. Epub 2010 Apr 8. Review. PubMed PMID: 20381467.
http://www.ncbi.nlm.nih.gov/pubmed/20381467

1: Zheng L, Qu L. Computational RNomics: structure identification and functional
prediction of non-coding RNAs in silico. Sci China Life Sci. 2010
May;53(5):548-62. Epub 2010 May 23. PubMed PMID: 20596938.
http://www.ncbi.nlm.nih.gov/pubmed/20596938

ncRNA, probe, GWAS

A method for automatically extracting infectious disease-related primers and probes from the literature
http://www.biomedcentral.com/1471-2105/11/410

Classification of ncRNAs using position and size information in deep
sequencing data
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2935403/?tool=pubmed

Forward-time simulation of realistic samples for genome-wide association studies
http://www.biomedcentral.com/1471-2105/11/442
Genetic drift or allelic drift is the change in the frequency of a gene variant (allele) in a population due to random sampling. The alleles in the offspring are a sample of those in the parents, and chance has a role in determining whether a given individual survives and reproduces. vs (natural selection)

In population genetics, linkage disequilibrium is the non-random association of alleles at two or more loci, not necessarily on the same chromosome. It is not the same as linkage, which describes the association of two or more loci on a chromosome with limited recombination between them. Linkage disequilibrium describes a situation in which some combinations of alleles or genetic markers occur more or less frequently in a population than would be expected from a random formation of haplotypes from alleles based on their frequencies. Non-random associations between polymorphisms at different loci are measured by the degree of linkage disequilibrium (LD). Numerically, it is the difference between observed and expected (assuming random distributions) allelic frequencies.

Detection and characterization of novel sequence insertions using paired-end next-generation sequencing.
http://bioinformatics.oxfordjournals.org/content/26/10/1277.full

Wednesday, October 27, 2010

imagemagick convert - split single multi-pdf to many pdfs

http://ardvaark.net/useful-pdf-imagemagick-recipes

Split single multi-pdf to many pdfs

$ convert -quality 100 -density 300x300 in.pdf multi%d.pdf

# combine, may increase in size by a lot
$ convert -density 150 pdf1.pdf pdf2.pdf out.pdf

or better
$ pdftk pdf1.pdf pdf2.pdf cat output temp.pdf

Tuesday, October 26, 2010

R aggregation

> x
j word journ
1 1    p     b
2 2    g     b
3 3    p     d
4 4    p     b
5 5    p     d
> with(x, tapply(word, journ, length))
b d
3 2

Monday, October 25, 2010

Perl monks for your PERL programming needs

http://www.perlmonks.org

Critical thinking

http://en.wikipedia.org/wiki/Critical_thinking

Critical thinking clarifies goals, examines assumptions, discerns hidden values, evaluates evidence, accomplishes actions, and assesses conclusions.
"Critical" as used in the expression "critical thinking" connotes the importance or centrality of the thinking to an issue, question or problem of concern. "Critical" in this context does not mean "disapproval" or "negative." There are many positive and useful uses of critical thinking, for example formulating a workable solution to a complex personal problem, deliberating as a group about what course of action to take, or analyzing the assumptions and the quality of the methods used in scientifically arriving at a reasonable level of confidence about a given hypothesis. Using strong critical thinking we might evaluate an argument, for example, as worthy of acceptance because it is valid and based on true premises. Upon reflection, a speaker may be evaluated as a credible source of knowledge on a given topic.
Critical thinking can occur whenever one judges, decides, or solves a problem; in general, whenever one must figure out what to believe or what to do, and do so in a reasonable and reflective way. Reading, writing, speaking, and listening can all be done critically or uncritically. Critical thinking is crucial to becoming a close reader and a substantive writer. Expressed most generally, critical thinking is "a way of taking up the problems of life."^[2]

Friday, October 22, 2010

Transcription factor, PROFESS, SPA

High Resolution Models of Transcription Factor-DNA Affinities Improve In Vitro and In Vivo Binding Predictions:http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000916

Semi-supervised recursively partitioned mixture models for identifying cancer subtypes

http://bioinformatics.oxfordjournals.org/content/early/2010/08/15/bioinformatics.btq470.full.pdf+html

PROFESS: a PROtein Function, Evolution, Structure and Sequence database: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2911846/
The advantage of the ‘answering queries using views’ approach to the database integration problem is that it reduces the integration problem to two steps: (i) building wrappers of the source databases, thereby providing simple ‘views’, and (ii) applying standard database queries on the views. Thus, implementing wrappers enables a robust query system that incorporates a variety of similarity functions capable of generating data relationships not conceived during the creation of the database. This will allow the user to move beyond simple text-based queries. Therefore, the PROFESS (PROtein Function, Evolution, Structure and Sequence) database uses wrappers to assist in the structural, functional and evolutionary analysis of the abundant number of novel proteins continually identified from whole-genome sequencing.
eggNOG http://eggnog.embl.de/
evolutionary genealogy of genes: Non-supervised Orthologous Groups

multiple structural alignment program, MAMMOTH-mult
http://ub.cbm.uam.es/mammoth/mult/

PROFESS
http://bionmr-c1.unl.edu/

Edit distance eg. kitten -> sitting has 3 character changes needed, useful for autocomplete
http://en.wikipedia.org/wiki/Levenshtein_distance

SPA: Short peptide analyzer of intrinsic disorder status of short peptides
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2900848/?tool=pubmed

Biological Insights of Transcription Factor through Analyzing ChIP-Seq Data
Kaida Ning, 2009

LaTeX, Sweave, R

\usepackage{hyperref}
\usepackage{tabularx}
\usepackage{listings}
\usepackage{graphicx}
\usepackage{url}
\usepackage{cite}

$ R CMD Sweave foo.Rnw ; texi2pdf foo.tex

http://www.stat.umn.edu/~charlie/Sweave/
http://www.stat.umn.edu/~charlie/Sweave/foo.pdf
http://www.stat.umn.edu/~charlie/Sweave/foo.Rnw

\pagebreak[3]
\verb@Sweave@

\begin{verbatim}
latex foo
\end{verbatim}

Figure~\ref{fig:one} (p.~\pageref{fig:one})

<>=
plot(x, y)
abline(out1)
@

\begin{figure}
\begin{center}
<>=
<>
@
\end{center}
\caption{Scatter Plot with Regression Line}
\label{fig:one}
\end{figure}

<>=
n <- 50
x <- seq(1, n)
a.true <- 3
b.true <- 1.5
y.true <- a.true + b.true * x
s.true <- 17.3
y <- y.true + s.true * rnorm(n)
out1 <- lm(y ~ x)
summary(out1)
@

The commands in package lattice have different behavior than the standard plot commands in
the base package: lattice commands return an object of class "trellis", the actual plotting is
performed by the print method for the class. Encapsulating calls to lattice functions in print()
statements should do the trick, e.g.:
<>=
library(lattice)
print(bwplot(1:10))
@

BibTeX and bibliography styles

http://amath.colorado.edu/documentation/LaTeX/reference/faq/bibstyles.html

The two Latex editors that I found most useful are:
1. Texmaker - lightweight, spell-check, have to press F1 and F3 to generate a PDF, need to click on the log window a lot
2. Kile - nicer, but I couldn't get syntax coloring to work for Sweave, spell-check, one-click gets you a PDF

Trick
- if you rename your '.Rnw' to '.tex' as a work around, it plays nicely with the editors
- then once all formatting is done, copy '.tex' to '.Rnw' and run the command
- or just create a tex symlink to Rnw! ln -s mydoc.Rnw mydoc.tex

R CMD Sweave mydoc.Rnw && texi2pdf mydoc.tex && evince mydoc.pdf

In R, call
> Stangle(file='foo.Rnw')
to extract the R code, WARNING: this will overwrite 'foo.R'!!!!!