신호와 의미 / Signal & Semantics

Photo 1. A toy car, a trial of out-focusing Yesterday I went to a photo studio, LemonTerrace Dongtan-branch , to take pictures of my son for celebrating the first birthday of him, " Dol ", a Korean word. The host of the studio, a specialist of camera, taught how to use my DSLR camera (EOS1000D) in details. Especially he demonstrated the out-focusing technique in case-by-case. A simple protocol for the beginner of DSLR user is the following; (1) Set 'Av' mode of your camera, (2) Set max number of ISO , my case is 1400, (3) adjust the distance between the camera and the subject as close as possible, (4) check shutter's speed by half pressing shutter button, (5) the speed should be lower than 1/60, (6) if too lower eg. 1/125, change ISO to be lower, (7) if higher speed, adjust the distance or set higher ISO, and (8) take a picture by full pressing. And he highly recommended for me to change my camera lens for portraits, 30 mm f/1.4 . The studio facilities and peo

Motivation Zhou et al . presented that an unique 30-amino-acid deletion in Nsp2-coding region is a key feature to classify whether a strain is a highly pathogenic porcine reproductive and respiratory syndrome virus (PRRSV). And the Nsp2, nonstructural protein 2, has been shown to undergo remarkable genetic variation, primarily in its middle region, while exhibiting high conservation in the N-terminal putative protease domain and the C-terminal predicted transmembrane region ( Han et al . 2007 ). This post aims to show how to find a quite large deletion in a specific coding-region with positional tolerance. Figure 1. The 30-Amino-Acid Deletion in the Nsp2 of Highly Pathogenic PRRSV.  ( Zhou  et al.  2009 ) Method and Implementation Pairwise alignment between a sequence of interest and a reference sequence (ORF1a of VR-2332 strain) is an essential step for finding insertions and/or deletions, shortly indels. The two sequences were aligned with BLAST (Altschul et al. 1999), e

Batch processing of beautifying phylogenetic trees I prefer to use treedyn when I decorate many number of phylogenetic trees at  one time. In use on Linux desktop, my Perl script works well to convert from raw trees to beautified trees. However,  it was stopped at running of treedyn because Tcl of treedyn essentially required a DISPLAY of X-Window when  the script was integrated into an Web application. Xvfb (X virtual framebuffer) presents a virtual screen for user or program, which works only on memory not real video device. And xvfb-run.sh , a script of Xvfb, is an utility for command line program. $ xvfb-run.sh my_script.pl -infile tree.phy -outfile tree.ps Please see details of xvfb-run.sh  in Dascalita's very concise post . Additional comments Chevenet, the author of treedyn, and Christen recently published ScripTree that is more flexible and functional program for script developers. This ScripTree is also required to use Xvfb in case of background execution without