My Blog

Formatting Database for Blast+ =========================== To use any sequence by Blast/Blast+ , we need to format the fasta . Let's do it  for uniprot: 1. download uniprot from the link provided ============================= ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.fasta.gz 2. issue the following command for blast+: ============================= /home/apps/ncbi/blast+/2.2.29/bin/makeblastdb -dbtype prot -in /path/to/uniprot.fasta To get blast+ commands, if you are familiar with legacy blast, use legacy_blast.pl in the following way: $ /home/apps/ncbi/blast+/2.2.29/bin/legacy_blast.pl formatdb -i test.fasta -p T --path /home/apps/ncbi/blast+/2.2.29/bin --print_only /home/apps/ncbi/blast+/2.2.29/bin/makeblastdb -dbtype prot -in test.fasta

http://www.ece.uci.edu/~chou/ssh-key.html Setting up SSH public/private keys SSH (Secure Shell) can be set up with public/private key pairs so that you don't have to type the password each time. Because SSH is the transport for other services such as SCP (secure copy), SFTP (secure file transfer), and other services (CVS, etc), this can be very convenient and save you a lot of typing. SSH Version 2 On the local machine, type the BOLD part. The non-bold part is what you might see as output or prompt. Step 1: % ssh-keygen -t dsa Generating public/private dsa key pair. Enter file in which to save the key (~/.ssh/id_dsa): (just type return) Enter passphrase (empty for no passphrase):

http://stackoverflow.com/questions/3587025/jfree-charts-sample-tutorial http://www.screaming-penguin.com/node/4005 http://www.vogella.de/articles/JFreeChart/article.html http://adityanivas3.blogspot.com/2008/09/jfree-chart-tutorial.html http://www.javaworld.com/javaworld/jw-12-2002/jw-1227-opensourceprofile.html There's even some examples right in the code, such as the one described here: http://www.jfree.org/jfreechart/api/javadoc/org/jfree/chart/demo/TimeSeriesChartDemo1.html  // HOW TO CREATE CHART AND SAVE AS PNG         final XYDataset dataset = createDataset();         final JFreeChart chart = createChart(dataset);                 try {             File f1 = new File("myline.png");             ChartUtilities.saveChartAsPNG(f1, chart, 500, 400);         } catch (Exception e) {             e.printStackTrace();         }

Open Control panel sudo  /opt/lampp/share/xampp- control-panel/xampp-control- panel How to start / stop apache server in xampp sudo /opt/lampp/lampp start sudo /opt/lampp/lampp stop How to change default apache port 80 to another port: Find the line "Listen 80" in any of these files and change to new port number. /opt/lampp/etc/httpd.conf /opt/lampp/etc/original/httpd. conf

1. Download you iso file. say myfile.iso 2. Make a directory where it will be mounted sudo mkdir /mnt/iso 3. Mount the iso file there sudo mount -t iso9660 -o loop /home/Download/myfile.iso /mnt/iso/     4. Install it   ./myfile.iso