.net 比较好的书
http://www.china-pub.com/301663
http://www.china-pub.com/43138
以后好好学
rails find method
@username = Company.find(:all, :conditions => ["nation=?", params[:q]])
@username = Company.find_all_by_nation(params[:q])
同时满足条件的：
@username = Company.find_all_by_nation_and_author_and_id(params[:q],”bb”,1)
LAMP（Linux + Apache + MySQL + PHP/Perl together commonly known as LAMP Server） 安装
LAMP（Linux + Apache + MySQL + PHP/Perl together commonly known as LAMP Server） 安装
在新立得软件包管理器中选择 编辑－－使用任务分组标记软件包
在打开的窗口中， 勾选 LAMP SERVER 然后确定
phpmyadmin 默认并不是安装在/var/www下面的，而是在/usr/share/phpmyadmin，你可以 把phpmyadmin复制过去，或者，网上有人说可以创建一个链接，然后把链接复制过去
sudo ln -s /usr/share/phpmyadmin /var/www/
在浏览器输入地址：http://localhost/phpmyadmin/
perl
sudo apt-get install libapache2-mod-perl2
/var/www 下面创建一个cgi-bin的文件夹：perl文件如下（1.pl）
#!/usr/bin/perl
print “Content-type: text/html\n\n”;
print “Hello, World.”;
http://localhost/cgi-bin/1.pl
sudo /etc/init.d/apache2 restart
/etc/apache2/apache2.conf
/etc/apache2/sites-available/default
ps:ScriptAlias /cgi-bin/ /usr/lib/cgi-bin/
<Directory “/usr/lib/cgi-bin”>
To this:
ScriptAlias /cgi-bin/ /var/www/cgi-bin/
<Directory “/var/www/cgi-bin”>
把编译好的primer3_core放到cgi－bin的文件夹下，并把primer3_results.cgi，primer3_www_results.cgi 中的/bin/nice
-19 ./primer3_core -format_output -strict_tags 改成/usr/bin/nice -19 ./primer3_core -format_output -strict_tags
sudo /etc/init.d/apache2 restart
TMHMM2.0 本地运行 ubuntu 8.04
1.官方去下载软件，用学术邮箱 http://www.cbs.dtu.dk/services/TMHMM/
2.把解压后的decodeanhmm文件放到/usr/bin/ 下面,(Make sure you have an executable version of decodeanhmm in the bin
directory.)
3.修改 tmhmm和 tmhmmformat.pl 中perl的运行路径 #!/usr/bin/perl;bin/tmhmm and bin/tmhmmformat.pl (if not /usr/local/bin/perl).
4.图形输出：需要For graphics, the package uses: gnuplot, ghostscript and ppmtogif.（其中ppmtogif在http://packages.ubuntu.com/ 中的Search the contents of packages：/usr/bin/ppmtogif netpbm，所以只要安装netpbm就可以了。）
比如说我需要命令dos2unix 或者ppmtogif 或者其他某些命令，我怎么才能知道这条命令是由哪个软件提供的呢？ 如果我不知道是哪个软件包，又怎么才能通过安装软件来使用命令呢？
5.修改：$gnuplot = "/usr/bin/gnuplot ";
$epsmove = "/sbin/grep -v \'translate\$\' ";
$ps2gif = "/usr/bin/gs -dNOPAUSE -q -sDEVICE=ppm -g710x350 -r72 -sOutputFile=- - -c quit | /usr/freeware/bin/ppmtogif - ";这些路径，为你程序运行环境的路径。
6.运行：./bin/tmhmm seq.fasta (possible:在上层的路径运行否则他找不到lib )
That all is ok!
transmembrane protein prediction
1.http://mendel.imp.ac.at/sat/DAS/DAS.html
"On filtering false positive transmembrane protein predictions": Miklos Cserzo, Frank Eisenhaber, Birgit Eisenhaber, and Istvan Simon; Protein Eng. 2002 15: 745-752. Please follow the link for the online abstract.
2.http://www.enzim.hu/hmmtop/index.html
HMMTOP is an automatic server for predicting transmembrane helices and topology of proteins, developed by G.E. Tusnády, at the Institute of Enzymology.
The method used by this prediction server is described in "G.E Tusnády and I. Simon (1998) Principles Governing Amino Acid Composition of Integral Membrane Proteins: Applications to Topology Prediction." J. Mol. Biol. 283, 489-506 (JMB) (Medline) (PDF).
The new features of HMMTOP 2.0 version is described in "G.E Tusnády and I. Simon (2001) The HMMTOP transmembrane topology prediction server" Bioinformatics 17, 849-850 (Bioinformatics) (Medline) (PDF).
3.http://www.cbs.dtu.dk/services/TMHMM-2.0/
This server is for prediction of transmembrane helices in proteins.
July 2001: TMHMM has been rated best in an independent comparison of programs for prediction of TM helices:
* S. Moller, M.D.R. Croning, R. Apweiler.
Evaluation of methods for the prediction of membrane spanning regions.
Bioinformatics, 17(7):646-653, July 2001. (medline)
Quote from the abstract:
`Our results show that TMHMM is currently the best performing transmembrane prediction program.'
TMHMM is described in
* A. Krogh, B. Larsson, G. von Heijne, and E. L. L. Sonnhammer.
Predicting transmembrane protein topology with a hidden Markov model: Application to complete genomes.
Journal of Molecular Biology, 305(3):567-580, January 2001.
(PDF, 959503 bytes)
* E. L.L. Sonnhammer, G. von Heijne, and A. Krogh.
A hidden Markov model for predicting transmembrane helices in protein sequences.
In J. Glasgow, T. Littlejohn, F. Major, R. Lathrop, D. Sankoff, and C. Sensen, editors, Proceedings of the Sixth International Conference on Intelligent Systems for Molecular Biology, pages 175-182, Menlo Park, CA, 1998. AAAI Press.
(Gzipped PostScript, 8 pages, 42470 bytes) (PDF, 844205 bytes)
bioinformatics source
http://en.dogeno.us/links/bioinformatics-tools-zz-google/
perl and bioperl大全
http://search.cpan.org/
bioperl Protein analysis tools
Signal localization tools
Protein domain identification
Summary statistics
- hydrophobicity
3D structure prediction
utf8 完整代码
CREATE DATABASE `protein6` DEFAULT CHARACTER SET utf8 COLLATE utf8_unicode_ci;
CREATE TABLE `protein6`.`westerns` (
`id` INT( 11 ) NOT NULL AUTO_INCREMENT ,
`预约日期` VARCHAR( 400 ) CHARACTER SET utf8 COLLATE utf8_unicode_ci NOT NULL ,
`预约人` VARCHAR( 400 ) CHARACTER SET utf8 COLLATE utf8_unicode_ci NOT NULL ,
`项目编号` VARCHAR( 400 ) CHARACTER SET utf8 COLLATE utf8_unicode_ci NOT NULL ,
`目的蛋白分子量` VARCHAR( 400 ) CHARACTER SET utf8 COLLATE utf8_unicode_ci NOT NULL ,
`tag抗体` VARCHAR( 400 ) CHARACTER SET utf8 COLLATE utf8_unicode_ci NOT NULL ,
`内参抗体` VARCHAR( 400 ) CHARACTER SET utf8 COLLATE utf8_unicode_ci NOT NULL ,
`自动生成的信息` VARCHAR( 400 ) CHARACTER SET utf8 COLLATE utf8_unicode_ci NOT NULL ,
`膜编号` VARCHAR( 400 ) CHARACTER SET utf8 COLLATE utf8_unicode_ci NOT NULL ,
PRIMARY KEY ( `id` )
) ENGINE = MYISAM CHARACTER SET utf8 COLLATE utf8_unicode_ci;
好了，就这样设置好了。
ruby 与 perl sub =~s///
#perl
$a=”23
21
32
4
23
4
32″;
$a =~s/\n.*//;
print “$a\n”;
#ruby
c = “111
23213
324
324
32
43
5
435
”
b = c.sub(/\n.*/,”XXXXXXXXX”)
puts b
\n.*就是把下一行替换掉