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Full Discussion: Improve the performance of my C++ code
Top Forums Programming Improve the performance of my C++ code Post 302931903 by Corona688 on Friday 16th of January 2015 10:01:08 AM
Old 01-16-2015
Quote:
Originally Posted by yifangt
My problem is the implementation. I want to step to "my second stage" of programming by using those available libraries.
"hash table" isn't exactly a library, it's different enough from other data structures it's often hand-rolled. Generalizing it too much would run the risk of poor performance, you need to pick the right algorithms for your application. It has a lot of restrictions as well (hard to iterate, deletion can cause something like fragmentation, and it can't be sorted). I've seen a few attempts at building a library for it, but nothing I ever liked very much.

In the end it's not that complicated. It's a big array with strict rules about what data gets put in what element. I'd suggest "open chaining" for your table -- basically an array full of lists -- with an index that's not really hashed at all, just converted from ACGT into boolean. Four letters would be 8 bits, for an array 256 long for example. Then you could just look up the first four letters of your sequence, find that list, and speedily check every possible thing which might contain your sequence without having to brute-force it.
Last edited by Corona688; 01-16-2015 at 11:24 AM..
This User Gave Thanks to Corona688 For This Post:
yifangt
 

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LEARN ABOUT DEBIAN

lastal

LASTAL(1)							   User Commands							 LASTAL(1)

NAME

       lastal - genome-scale comparison of biological sequences

SYNOPSIS

       lastal [options] lastdb-name fasta-sequence-file(s)

DESCRIPTION

       Find local sequence alignments.

       Score  options  (default  settings): -r: match score   (DNA: 1, protein: blosum62, 0<Q<5:  6) -q: mismatch cost (DNA: 1, protein: blosum62,
       0<Q<5: 18) -p: file for residue pair scores -a: gap existence cost (DNA: 7, protein: 11, 0<Q<5: 21) -b: gap extension cost  (DNA:  1,  pro-
       tein:   2,  0<Q<5:   9)	-c:  unaligned	residue  pair cost (100000) -F: frameshift cost (off) -x: maximum score drop for gapped alignments
       (max[y, a+b*20]) -y: maximum score drop for gapless alignments (t*10) -z: maximum score drop for final gapped alignments  (x)  -d:  minimum
       score for gapless alignments (e*3/5) -e: minimum score for gapped alignments (DNA: 40, protein: 100, 0<Q<5: 180)

       Cosmetic  options  (default  settings): -h: show all options and their default settings -v: be verbose: write messages about what lastal is
       doing -o: output file -f: output format: 0=tabular, 1=maf (1)

       Miscellaneous options (default settings): -s: strand: 0=reverse, 1=forward, 2=both (2 for DNA, 1 for protein) -m: maximum multiplicity  for
       initial	matches (10) -l: minimum length for initial matches (1) -n: maximum number of gapless alignments per query position (infinity) -k:
       step-size along the query sequence (1) -i: query batch size (1 MiB if Q>0, else 16 MiB if j=0, else 128	MiB)  -u:  mask  lowercase  during
       extensions: 0=never, 1=gapless,

	      2=gapless+gapped but not final, 3=always (2 if lastdb -c and Q<5, else 0)

       -w:  supress  repeats  inside exact matches, offset by this distance or less (1000) -G: genetic code file -t: 'temperature' for calculating
       probabilities (1/lambda) -g: 'gamma' parameter for gamma-centroid and LAMA (1) -j: output  type:  0=match  counts,  1=gapless,  2=redundant
       gapped, 3=gapped,

	      4=column ambiguity estimates, 5=gamma-centroid, 6=LAMA (3)

       -Q: input format: 0=fasta, 1=fastq-sanger, 2=fastq-solexa, 3=fastq-illumina,

	      4=prb, 5=PSSM (0)

REPORTING BUGS

       Report bugs to: last (ATmark) cbrc (dot) jp
       LAST home page: http://last.cbrc.jp/

lastal 199							     May 2012								 LASTAL(1)
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