Documentation:

Automated splice site analyses compiles mutation data from wide variety of sources that result in genetic disorders.

The procedure of executing Automated splice site analysis is as follows:
input file:

It contains three lines.
First line correponds to the location of the mutation datafile.
Second line corresponds to the location where exon coordinates are being stored.
Third specifies about the cds position. If it starts with a '0' then, the cds start should not be added to get the nucelotide position, if '1', then the cds start should be added to obtain the correct location of the nucleotide refering to.

example: input file

database/COL1A2.txt
exoncoor.txt
1

eein file:

The first line specifies the accession number
The second line specifies the mrna.txt file to be used
The third line specifies the chromosome number
The fourth line, specifies the location where the output files have to be stored. It serves as a purpose for name of gene too.
The fifth line, specifies the link to the mutation table
The sixth line, specifies the link to genbank entry
The lines following  specify the references.

Z74616
/pharmcogen/genomes/human/apr03/chrm_7/mrna.txt
chrm_7
EDATA/COLIA2
http://www.le.ac.uk/genetics/collagen//col1a2.html
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=nucleotide&list_uids=1418929&dopt=GenBan
k
database of human type I and type III collagen mutations


ee.pl
input : eein
output : exoncoor.txt
It reads the accession number mentioned in the eein.
The codon start position ( cds) is identified from the mrna text mentioned.
The exon boundaries are calcucated in the mrna text file and the output is kept in the file exoncoor.txt.

new.pl

input: input, eein, exoncoor.txt, instp
output: inst, mut_list

Its reads the accession number from the eein file.
It reads the mutation data file.
Each mutation represented in the data file is converted to delila instruction.
This program is individually executed for acceptor and donor with differenet Ribl matrix, so that different inst values are generated for acceptor and donor.
The range of the window used in the delila instruction will be equal to twice of the length of Ribl matrix used.
mut_list contains the natural splice sites relative to the mutation taking place.
If the mutation takes place in the middle of the exon,  then natural splice site is not located and termed as NA ( non applicable).

run2.splice

input: exon.pl
output: pop.html, natural.txt
other programs used: natural.pl, popup.pl, delila, scan

This is a bash script used to generate pop.html, a file which contains information content of the natural sites. The exoncoor.txt ( output from ee.pl) is used as input. File natural.txt contains the locations of the natural sites. After the extraction of natural sites, instructions are formed, delila is executed. The scanp value is reduced to a very low value and  the book obtained from delila is scanned. The pop.html containing the information content is generated using popup.pl

delila

Delila is run separately for donor and acceptor. More information about delila can be had from the link.

real.pl

input: data , eein
output: increased.html, decreased.html, equal.html, gene.html, increased.txt, decreased.txt, equal.txt


The chromosome, gene are read from the eein file. The output files are stored in the directory named by the gene name.
The data file is scanned and all the changes in the information content values are categorized according to the type of change as increased, decreased and nochange. The changes are tabulated in the html files i.e increased, decreased, and nochange.
All the changes observed, when scanned either under donor or acceptor are tabulated under separate tables "total" under donor and acceptor.
sort.pl

input: increased.txt, decreased.txt, equal.txt
output: sort_list.html

All the changes both under donor and acceptor in information content observed are tabulated according to the mutation made.

popup.pl

input:  natural.txt, data
output: pop.html

It generates a html file containing information content of natural sites.

natural.pl

input: exoncoor.txt
output: natural.txt

It generates the list of natural sites found in the accession number

genhtml.pl

output: menu.html, donor.html, acceptor.html

It generates a list of menus for donor and acceptor.