Highlight syntax color code

http://www.andre-simon.de/doku/highlight/en/highlight.html

EST

to map ESTs and variable reads (multiple fasta-format files) to an already known related prokaryotic genome

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2789075/

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

The current commercially available high-throughput methodologies rely on primers or probes designed to detect each of the current reference miRNA sequences residing in miRBase, which acts as the central repository for known miRNAs (Griffiths-Jones 2006).

However, probe-based methodologies are generally restricted to the detection and profiling of only the known miRNA sequences previously identified by sequencing or homology searches.

Sequencing-based applications for identifying and profiling miRNAs have been hindered by laborious cloning techniques and the expense of capillary DNA sequencing (Pfeffer et al. 2005; Cummins et al. 2006).

In contrast with capillary sequencing, recently available “next-generation” sequencing technologies offer inexpensive increases in throughput, thereby providing a more complete view of the miRNA transcriptome.

Pluripotent human embryonic stem cells (hESCs) can be cultured under nonadherent conditions that induce them to differentiate into cells belonging to all three germ layers and form cell aggregates termed embryoid bodies (EBs) (Itskovitz-Eldor et al. 2000; Bhattacharya et al. 2004).

Samples of undifferentiated hESCs and differentiated cells from EBs were chosen for miRNA profiling, first because the pluripotency of ESCs is known to require the presence of miRNAs (Bernstein et al. 2003; Song and Tuan 2006; Wang et al. 2007) and second because specific changes in miRNA expression are thought to accompany differentiation (Chen et al. 2007).

These reads were mapped to the genome by forcing perfect alignments beginning at the first nucleotide and retaining the longest region of each read that could be aligned to the reference genome, along with all alignment positions. After mapping, a total of 766,199 (hESC) and 724,091 (EB) unique error-free trimmed small RNA sequences were represented by 4,351,479 and 3,886,865 reads.

Sequences deriving from 334 distinct miRNA genes were identified. The miRNAs were the most abundant class of small RNAs on average, but spanned the entire range of expression, with sequence counts up to ~120,000 (Fig. 1A).

Virtually no reads aligned to the genome after position 28, so we trimmed all reads at 30 nt to reduce the number of unique sequences.

For every read, the longest alignment was determined, and this subsequence, as well as the positions for every alignment of this length, was stored in a database (to a maximum of 100 alignments). 

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2279248/?tool=pubmed

Nanopore sequencing

http://www.youtube.com/watch?v=HbjAMJehSlg&feature=related

Perl database interface DBI

http://www.perl.com/pub/1999/10/DBI.html
# db settings
my $db = "mydbname";
my $host = "127.0.0.1";
my $port = 3306;

# connect
my $dsn = "DBI:mysql:database=$db;host=$host;port=$port";
my $fosdb = DBI->connect( $dsn, $user, $pass) or die ( "Couldn't connect to database: " . DBI->errstr . "\n";

# Read the matching records and print them out          
          while (@data = $sth->fetchrow_array()) {
            my $firstname = $data[1];
            my $id = $data[2];
            print "\t$id: $firstname $lastname\n";
          }

my $sth = $dbh->prepare('SELECT age FROM people WHERE id = ?')
            or die "Couldn't prepare statement: " . $dbh->errstr;

$sth->execute($id) 
            or die "Couldn't execute statement: " . $sth->errstr;

$dbh->disconnect;

perlconsole - An interactive Perl console like Python's

Installing the package libterm-readline-gnu-perl should get you readline support. 

$ apt-cache show perlconsole
...
Description: small program that lets you evaluate Perl code interactiv
+ely
 Perl Console is a light program that lets you evaluate Perl code
 interactively. It uses Readline for grabing input and provides comple
+tion
 with all the namespaces loaded during your session.
 .
 This is pretty useful for Perl developers that write modules.
 You can load a module in your session and test a function exported by
+ the
 module.

http://www.perlmonks.org/?node_id=816352

MiPred

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1933124/

In this article, in order to achieve higher performance of distinguishing the real pre-miRNAs from the pseudo ones, a hybrid feature by incorporating the local contiguous structure-sequence composition, the minimum of free energy (MFE) of the secondary structure and the P-value of randomization test was used.

Genotype calling

www.cbs.dtu.dk/chipcourse/Lectures/genotype_calling.pdf

SNP call rate?  Plot of SNPs along allele A (eg. A) and allele B (eg. C) 

You can either get AA (AA), AB (AC), or BB (CC).

R draw.key positioning

https://stat.ethz.ch/pipermail/r-help/2009-February/187229.html

The simplest way to change position is to supply a simple 'vp' argument.

xyplot(1~1,
       panel = function(...) {
           require(grid)
           panel.xyplot(...)
           draw.key(list(text=list(lab='catch'),
                         lines=list(lwd=c(2)),
                         text=list(lab='landings'),
                         rectangles=list(col=rgb(0.1, 0.1, 0, 0.1))),
                    draw = TRUE,
                    vp = viewport(x = unit(0.75, "npc"), y = unit(0.9, "npc")))
       })

MiR-107 and MiR-185 Can Induce Cell Cycle Arrest in Human Non Small Cell Lung Cancer Cell Lines

MiR-107 and MiR-185 Can Induce Cell Cycle Arrest in Human Non Small Cell Lung Cancer Cell Lines

http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0006677

Algorithm text books

• the book "Biological sequence analysis" by Durbin et al. (Cambridge University Press, ISBN-13: 978-0521629713) will serve as our main reference book (the BSA book)
• if you do not have a strong Biology background, I suggest "Molecular Biology of the Gene" by James Watson et al. (Benjamin Cummings, 6th edition (2007), ISBN-13 978-0805395921) and, to a lesser extent, "Molecular Biology of the Cell" by Bruce Alberts which is also a fine book (Garland, 4th edition (2002), ISBN-13: 978-0815332183) as your reference books. Make sure you are dealing with the latest editions of these books.

http://www.cs.ubc.ca/~irmtraud/cs_545/

Analytic Bridge

Data mining, statistics, quant, operations research, six sigma, econometrics, web analytics, text mining, business intelligence, SAS, biostatistics, machine learning, artificial intelligence, decision sciences, cloud computing, SaaS.

http://www.analyticbridge.com/

Deep Sequencing - sequence coverage

http://scienceblogs.com/mikethemadbiologist/2010/03/what_is_deep_sequencing.php

Git basics

Upload it again: 'git push'
So, to have a successful work session do the following:
   Sit down at computer
   type 'git pull'
   make changes
   test your changes
   type 'git commit'
   describe your changes
   type 'git pull'
   type 'git push'
   Get up and walk away from the computer

You can type 'git pull' every minute, if you like.
You can type 'git commit -a' just after you've
made a change and
have tested it a little (Any syntax errors?
Does it run at all?).
You can type 'git push' after each commit; it has
no effect until then.


~$ git config --global user.email my@email.com
~$ git config --global user.name myusrname