Stormo Lab Publications RSSVM with bibtex

http://ural.wustl.edu/pubs.html

Common R Mistakes

http://www.springerlink.com/content/x730205j9241l531/

Can't write to usb drive

1. check physical write protect on usb drive

It is quite clear that your disk is 1) full and 2) damaged.

OPTION 1: Repair

* restore the file system running "dosfsck -a /dev/sdb1"

The -a option will automatically repair the errors to make the filesystem consistent again. Lost clusters will be converted to files and keep taking space. Perhaps also space will be freed. After running the disk check, run "df -h /dev/sdb1" again to check the free space. Chances are it will already be more than 1% (I added the -h swicht, means "human readable) to have sizes displayed in kB, MB). After that, clean up the drive, deleting what isn't necessary.

OPTION 2. Reformat altogether

sudo umount /dev/sdb1
sudo mkfs -t vfat /dev/sda1

Warning: You are probably aware that reformatting destroys all data on the disk !

Dr. Seuss' Quotes

I meant what I said and I said what I meant.

I like nonsense; it wakes up the brain cells.

# Be who you are and say what you feel because those who mind don't matter and those who matter don't mind.

# Today was good. Today was fun. Tomorrow is another one.

# You know you're in love when you can't fall asleep because reality is finally better than your dreams.

http://quotations.about.com/od/bookquotes/a/seuss1.htm

Trees and Strength - J. Willard Marriott

"Good timber does not grow with ease; the stronger the wind, the stronger the trees."

Episode Ratings

http://wiki.d-addicts.com/I_Believe_in_Love/Episode_Ratings

Flash Player Square for Ubuntu 64

http://labs.adobe.com/downloads/flashplayer10_square.html

Multiz Threaded-Block-Alignment

http://www.ncbi.nlm.nih.gov/pubmed/15060014
    MULTIZ uses pairwise alignments produced by BLASTZ. These are filtered to select the best match in the genome, so that each base in human aligns to a single base in the other species. We tried two different methods to filter these alignments, axtBest (Schwartz et al. 2003a) and the “net” approach described in Kent et al. 2003. In general axtBest aligns slightly more human bases, and the net approach is somewhat better at identifying orthologs. We prefer the latter.

http://www.bx.psu.edu/miller_lab/
http://www.bx.psu.edu/miller_lab/dist/tba_howto.pdf

The starting material for running TBA includes:
1. A set(s) of sequences from different species
2. An evolutionary tree describing the relationship of these species
3. A parameter file describing how to run blastz for different species. For example,
you might want to treat alignments involving non-placental mammals differently
from placental mammals. This file is optional.

3 Overview of running TBA
There are typically three steps involved with generating a multiple alignment:
1. generating a series of pair-wise alignments to “seed” the multiple alignment process (This process is performed with the program all bz, which is essentially a program that executes a series of blastz commands., outputs a "lav" format that is converted to MAF)
2. generating the multiple alignment (tba, calls multiz)
3. “projecting” the alignment onto a reference sequence

http://genome.csdb.cn/cgi-bin/hgTrackUi?hgsid=446052&c=chrX&g=mostConserved28way

Trails - George Bernard Shaw

"Do not follow where the path may lead. Go instead where there is no path and leave a trail."

George Bernard Shaw 

Tools for managing and analyzing microarray data

http://bib.oxfordjournals.org.proxy.lib.sfu.ca/content/early/2011/03/20/bib.bbr010.full.pdf+html

Top 100 Fantasy Movies

http://www.fantasybooksandmovies.com/best-fantasy-movies.html

Top 10 Best Cinematography Films

http://www.runningwithscissors.com/top-10-best-cinematography-films

http://moviemaniac14.blogspot.ca/2011/03/top-10-movies-with-best-cinematography.html

HOME (homeproject)
http://www.youtube.com/watch?v=jqxENMKaeCU&list=PLECFB679284982CA6&feature=plpp

Repeats

http://rsat.ulb.ac.be/help.retrieve-ensembl-seq.html
The presence of repetitive elements hampers the detection of motifs, especially for vertebrate genomes, because these repetitive sequences have a very distinct composition than the rest of the genome.

http://genes.mit.edu/Repeats.html
The presence of certain types of repetitive elements in a sequence may sometimes distort the results of GENSCAN. In particular, L1 elements are often predicted as genes. To avoid this potential problem, you may wish to pre-screen for repetitive elements with a program like RepeatMasker or censor which replace sequence segments matching any of a set of elements common to your organism (e.g., Alu, L1, etc.) by the same number of asterisks or `N's.

Another option is to filter out repeats after running GENSCAN, e.g. to screen GENSCAN predicted peptides against a database of repeat sequences translated in all six frames.

Rogozin et al. Brieifings in Bioinformatics. 2000
This model suggests that
most SINEs in the mammalian
genomes are pseudogenes, and not
capable of producing copies.


SINE can affect the
function and
recombination of
surrounding sequences


Thus, insertions of SINEs (as
well as other types of genome
mutations) can affect the long-term
adaptability of the species in various
ways.1,58



The database of repetitive elements
(Repbase)66


SINEs are almost always
a signture of non-coding
DNA



Incomplete SINEs or highly divergent
sequences can create some problems for
prediction.



Undiscovered repetitive elements, in
poorly characterised genomes, can
create serious problems for computational
functional mapping of sequences.


The presence of repetitive elements can
create serious problems for sequence
analysis, especially in homology
searches in nucleotide sequence
databases. It is difficult to interpret
database search results if the output is
saturated by a number of highly scored
matches with repetitive elements which
are widely present in nucleotide
sequence databases.