Work+092412

There is an error with how MotifGroup extracts its own information so I need to go back and fix this part. Then I can move on to adding bepipred functionality, and then blast functionality.

1143 finished fixing MotifGroup. Now I can add bepipred functionality. First I need to install bepipred.

downloaded bepipred and tried to follow instructions here http://www.cbs.dtu.dk/services/doc/bepipred-1.0.readme

I changed the paths like they told me to. I don't know if the "sticky" bit was set on tmp or not. received the following error when running ./bepipred in the appropriate directory in cygwin /bin/tcsh: bad interpreter: Permission denied This site seemed to know the problem. http://www.linuxquestions.org/questions/linux-newbie-8/bin-csh-bad-interpreter-175062/ So then I tried to install the tcsh shell by following the instructions here http://cs.nyu.edu/~yap/prog/cygwin/FAQs.html However, after following the instructions and then starting the cygwin that should use tcsh, the shell just opens and closes. This process seems daunting. Maybe I will try to install blast and get that working instead.

I found out how to check the sticky bit. ls -ld /tmp this gives a result like drwxrwxrwt+ 1 kwhittem Domain Users 0 Sep 23 11:57 /tmp the sticky bit is represented by the letter **t** in the final character-place

Kevin helped me get a little farther

Oh okay I now have the program working a little farther. I reinstalled Cygwin so that it would install more shells. I then added the following code to the Bepipred file. However, now when running ./bepipred I receive the following error message.

bepipred: no "fasta2proppred" executable for CYGWIN_NT-5.1-i686

Kevin wrote a program to run Bepipred by calling the website. However, their website has changed and his program no longer works. Here is the directory of his program. S:\Administration\software\custom software\IEDB Analysis

Here's an example command and some output C:\Documents and Settings\kwhittem\My Documents>"S:\Administration\software\cust om software\IEDB Analysis\ImmepRetrieveBepipred.exe" --file=..\Desktop\temp\test .fa --output=output.txt Epitopes Predicted: 0

It looks like the best solution for Bepipred is to run it on Linux (perhaps in a virtual box), and then call commands to this Linux machine. see this e-mail from Kristoffer Rapacki https://mail.google.com/mail/u/0/?ui=2&shva=1#label/Career/139fa12684148679

Okay onto blast

How to: Run BLAST software on a local computer http://www.ncbi.nlm.nih.gov/guide/howto/run-blast-local/

Blast can be downloaded here: ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ All of the databases for blast can be updated with this command

./update_blastdb.pl htgs as seen here

http://www.ncbi.nlm.nih.gov/books/NBK1763/#CmdLineAppsManual.3_Quick_start or individual databases can be installed

ftp://ftp.ncbi.nlm.nih.gov/blast/db/ For example, one might just want to download the nr database for the non-redundant sequences

I'm having trouble getting blast setup. It looks like this website might help me. http://www.blaststation.com/freestuff/en/howtoNCBIBlastWin.html

Alright now it works. I just had to call the database nr.00 since that's what the downloaded database files were called rather than just nr.

Here's an example command: C:\cygwin\home\kwhittem\NCBI\blast-2.2.27+\bin>blastp -db nr.00 -query test_fast a.fsa -out results.out

When I try to blast with a short query sequence such as "pqregs" no hits are found. Therefore, I need to find out how to blast short query sequences. Tried psiblast. This does not find short input sequences.

To do a short query blast I can use the regular blast program, but change the parameters. This page describes the process. http://www.ncbi.nlm.nih.gov/blast/Why.shtml This table shows how this should be done.
 * **Program** || **Word Size** || **Filter** || **E Value** || **Composition based Statistics** || **Score Matrix** ||
 * Standard protein BLAST || 3 || On (SEG) || 10 || On || BLOSUM62 ||
 * Search for short/nearly exact matches || 2 || Off || 20000 || Off || PAM30 ||

Here are some BLAST parameters I might be interested in. [-word_size int_value] [-evalue evalue] [-threshold float_value] //I'm probably interested in evalue rather than threshold [-num_descriptions int_value] [-num_alignments int_value] [-matrix matrix_name]

Actually the best way to search with short queries is probably to just set the task parameter -task task_name e.g. -task blastp-short this page describes this http://www.ncbi.nlm.nih.gov/books/NBK1763/

using -task blastp-short did not yield results, but searching like this ./blastp -db nr.00 -query pqregs.fsa -word_size 2 -evalue 20000 -num_descriptions 20000 -matrix PAM30 -out results.out did.

blastp parameter descriptions

Before I found the parameter descriptions I was in the process of writing the blast help desk an e-mail. It looks like I don't need to send this e-mail any longer though. Blast help desk email 9-25-12

This command has all of the parameters set correctly and gave me lots of results for a short query sequence ./blastp -db nr.00 -query pqregs.fsa -word_size 2 -seg no -evalue 20000 -comp_based_stats 0 -matrix PAM30 -num_descriptions 20000 -out results.out

I can also take away all of the alignments at the bottom of the text file. ./blastp -db nr.00 -query pqregs.fsa -word_size 2 -seg no -evalue 20000 -comp_based_stats 0 -matrix PAM30 -num_descriptions 20000 -num_alignments 0 -out results.out

I think this is the command I'll use for the final command in my program.

Here is an example about how to blast or align two proteins against eachother. ./blastp -subject test_fasta3.fsa -query test_fasta4.fsa -out results3.out

Now that I know that I can get BLAST setup and working, I can try to get Bepipred working on a Linux virtual box that I can reach with ssh on the same windows computer that the virtual box is running on.

My Cygwin did not already have ssh by default. I am reinstalling it with the appropriate packages according to the directions here: http://animatedlight.net/node/2

I ended up getting a virtualbox with linux with bepipred controlled by ssh by cygwin up and running.

Now I would like to know how to copy files with ssh. info from http://hintsforums.macworld.com/archive/index.php/t-29244.html copy from a remote machine to my machine: scp user@192.168.1.100:/home/remote_user/Desktop/file.txt /home/me/Desktop/file.txt

copy from my machine to a remote machine: scp /home/me/Desktop/file.txt user@192.168.1.100:/home/remote_user/Desktop/file.txt

copy all file*.txt from a remote machine to my machine (file01.txt, file02.txt, etc.; note the quotation marks: scp "user@192.168.1.100:/home/remote_user/Desktop/file*.txt" /home/me/Desktop/file.txt

copy a directory from a remote machien to my machine: scp -r user@192.168.1.100:/home/remote_user/Desktop/files /home/me/Desktop/.

How do I exit ssh? just type exit

Okay I now have all of the programs up and operational. Now I need to code my Java program to use these programs.