Multiple Sequence Alignment by Parallel Iterative Aligner(KL1,C)

1) Abstruct

We have studied application systems for parallel inference machine developed 
in ICOT. The systems analyze protein sequences and generate multiple sequence 
alignment. That analysis is very important in the field of genetic information 
processing. Multiple sequence alignment is useful for predicting structure and 
function of protein, DNA, and RNA, and for estimating the evolutionary relationships 
among creatures. The tree-based method, widely adopted as an alignment algorithm, 
tends to accumulate errors when aligning sequence of low similarities. It was 
recently found that iterative improvement could correct such errors, but that 
too many iteration cycles were needed to solve a practical-scale problem. 


2) Environment

Machine     : Parallel machin based on UNIX
Environment : KLIC,UNIX,gcc(cc)
Language    : KL1,C
Source Code : 190KB


3) Files

2dp_new_klic.h

alignment_string.c
cost_b.c
cost_s.c
dist_b.c
dist_s.c
gdp.c
generateD_b.c
generateD_s.c
keep_memory_b.c
keep_memory_s.c
make_prof.c
matrix_amino.c
minimum_b.c
minimum_s.c

chk_outg.kl1
converter-2.kl1
cp1.kl1
dayhoff3.kl1
energy.kl1
kl1-part-2.kl1
main_c_new3.kl1
pia_c_s1_n.kl1
rechk_outg.kl1
top-2.kl1

compile
data17
data17.res


4) How to install

Please see "INSTALL_p".


5) How to use

Please see "INSTALL_p".


