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Iam plogging using a wiki now. I have still not decided to make it public or not (bcos I dont want ppl to modify my stuff!)!

plog - Project log

All the blah-blah-blah of the research being done by Suresh Solaimuthu aka BULL.

103003

Completed the experiments for Aquifex aeolicus(AE000657) after such a long long time. Mostly because it was manual most of times. Now Iam writing codes to automate it. The analysis are going on.

There was a long gap not in the stuffs but I was lazy writing them!!!!!

Again I have started to write.

072303

Showed the professor the results obtained and the latest modification. Found a bug!!!!!! For the second coding sequence the random synonomous sequeces are more than double the size of the actual coding sequence!!!!! Probably this is the error in the usage of array!!!!! Looking into the bug.

072203

Ran the program of 072103 for just first two coding sequences of Aquifex aeolicus. Modified the programs for some of the bugs.

072103

Made some changes to the code to generate the sequences. Included provisions to check the divisibility of 3 of the length of sequence.

072003

Same as above.

071903

Nothing much done.

071803

Got codon usage for some more bacterias as done on 071503.

071703

Wrote a code to get all the coding sequences for all the organisms and stored in the respective organism directory.

Modified the code to generate the random synonomous sequences for all the sequences generated by the above.

071603

Started generating the synonomus sequences.

Had meeting with Professor and complained about the time it takes to generate the synonomous random sequences. Professor asked to generate the sequences for individual coding sequences and not for the entire organism!!!!!!!!!

Also we decided to have all the possible checks to-be-done by the program like if the sequences has proper codons(the length divisible by 3), etc......

071503

Got the codon usage from http://www.kazusa.or.jp/codon/ for two bacterias.

Wrote a perl code to convert the codon usage table into suitable format. The temporary file created by the program will have the probability distribution of the codons.

Completed the code for synonomous sequence generation.

071403

Started the plog officially.

Collected all the sequeces for the bacterias from the NCBI site. ftp://ftp.ncbi.nih.gov/genbank/genomes/Bacteria/

Started the codes for the synonomous sequence generation for the above sequences.