linux grep color setting

1. Solution
alias grep_gray="GREP_COLOR='1;30' grep --color=always"
alias grep_red="GREP_COLOR='1;31' grep --color=always"
alias grep_green="GREP_COLOR='1;32' grep --color=always"
alias grep_yellow="GREP_COLOR='1;33' grep --color=always"
alias grep_blue="GREP_COLOR='1;34' grep --color=always"
alias grep_magenta="GREP_COLOR='1;35' grep --color=always"
alias grep_cyan="GREP_COLOR='1;36' grep --color=always"

2. Example
echo hello there | grep_magenta ll | grep_yellow ere
hello there



Reference:
detail
linux color tutorial

Centos linux etc system config

1. Introduction

This is the nerve center of your system, it contains all system related configuration files in here or in its sub-directories. A "configuration file" is defined as a local file used to control the operation of a program; it must be static and cannot be an executable binary. For this reason, it's a good idea to backup this directory regularly. It will definitely save you a lot of re-configuration later if you re-install or lose your current installation. Normally, no binaries should be or are located here. [detail]

2. Category

[Network]
Firewall:  /etc/sysconfig/iptables , service iptable restart
DNS server: /etc/resolv.conf


[File System]
Files system: /etc/fstab, mount -a
Auto mount: /etc/auto.mnt, /etc/auto.master, service autofs restart

Javascript detect browser type

1. Problem:

Sometimes there are different present in the different browser, especially in IE and firefox-like. In this we should get the browser type and do the different method

2. Solution

/* To get the browser type */
function detectIsIEBrowser(){
    var isIE = false;
    var val = navigator.userAgent.toLowerCase();
   
    if(val.indexOf("msie") > -1) {
        isIE = true;
    }
    return isIE;
   
}




Reference
Basic
Advance_PPK

YUM Repository

1.The YUM path
 YUM is a easy management software tools, and mostly the
repository  files will in /etc/yum.repos.d/ and the config file in /etc/yum.conf

2. Useful yum commands

• yum search tools-name
• yum install tools-name
• yum info tools-name
• yum list installed
• yum clean

3.  Useful yum repository

in my CentoOS 6.2, I use the following repo

• CentOS-Base.repo
• CentOS-Debuginfo.repo
• CentOS-Media.repo
• mirrors-rpmforge
• mirrors-rpmforge-extras
• mirrors-rpmforge-testing
• rpmforge.repo

4.  Advance isuuses

• How to new a repository??
• Taiwan's usefully repository.

CLC Bio about NGS develop

RNA Ploy A tail

From: Ploy(A) Tail

The Poly(A) Tail

As illustrated in the following figure, a generic messenger RNA (mRNA) consists of a number of distinct features, each of which has different functions. The very 5’-end* of the mRNA has a so-called cap (the chemical structure of which is shown in the figure). The most recognizable part of the mRNA is the open-reading frame; this is the series of nucleotides that are “read” by ribosomes to yield the polypeptide that is coded by the mRNA. The open reading frame begins (almost always) with the nucleotide triplet AUG, and ends (after a number of nucleotides that is a multiple of three) with one of the three “stop codons” (UAA, UAG, UGA). At the 3’-end* lies a tract of adenosines – between 90 and 300 or so, at the outset of the life of an mRNA. Finally, the regions of the mRNA between the cap and open reading frame, and between the open reading frame and poly(A) tail, are designated as the 5’- and 3’- untranslated regions, or UTRs.

These different features all interact with other cellular factors; the complete story fills large review volumes, and I won’t bother to try and describe everything. However, it is important for this overview to note that the cap is bound by a so-called cap-binding complex, and the poly(A) tail by a poly(A)-specific RNA binding protein (the poly(A)-binding protein, or PAB). As a single PAB binds only 12 or so nucleotides, the poly(A) tail is “coated” with a number of PAB subunits.

The poly(A) tail functions in two ways. It promotes translation of the mRNA by ribosomes, via a process that is briefly sketched in the following figure. The poly(A) tail, via PAB, actually is “connected” with the cap of the mRNA, via interactions of PAB and the cap-binding complex with other translation initiation factors. This serves to circularize the mRNA-protein complex as shown, and to stabilize the interactions at the 5’-end of the mRNA. The cap-binding complex and other translation initiation factors eventually recruit the small (40S) ribosomal subunit to the vicinity of the cap; this subunit and some of the initiation factors then scan along the mRNA until it finds a suitable AUG triplet, whereupon the 60S ribosomal subunit, initiator tRNAs, and other factors come into play to begin the process of translation.

Remove or unlink the symbolic link

1. What ??
General I often to use the unlink to remove the symbolic links,
but when there are many links file in a folder,
is there any of quick method to do that ??



2. Solution:
A. Write a batch to unlink the symbolic link.

B. Use rm when there are no any physical files in this
rm reference

      If file is a symbolic link, then only the symbolic link is removed.
      The file or directory pointed to by the symbolic link is not affected.
      If any of the intermediate path components of file happens to be a
      symbolic link, then rm follows the symbolic link and removes the file.

Reference: How to Unlink all files in a directory?