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Full Discussion: Improve the performance of my C++ code
Top Forums Programming Improve the performance of my C++ code Post 302931813 by Corona688 on Thursday 15th of January 2015 03:52:31 PM
Old 01-15-2015
Quote:
Originally Posted by yifangt
corona688, can I make sure the difference between list<> and vector <> can be hours?
Vector is not "fast" and list is not "slow".

If you try to insert in arbitrary places anywhere inside a vector, it will be slow.

If you try to use a list for random access, it will be slow.

What I have suggested is better suited for lists than vectors.

Quote:
I must have missed something big for my code.
You are comparing every element to every other element. If you have 300 elements, that's 90,000 comparisons. If you have 3000 elements, that's 9 million comparisons. Any sequence you remove early means 300 fewer loops later.

You are also searching for strings inside strings without using any sort of index, but that would be complicated.
Last edited by Corona688; 01-15-2015 at 04:59 PM..
This User Gave Thanks to Corona688 For This Post:
yifangt
 

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LEARN ABOUT DEBIAN

clustalo

clustalo(1)							   USER COMMANDS						       clustalo(1)

NAME

       clustalo - General purpose multiple sequence alignment program for proteins

SYNOPSIS

       clustalo [-h]

DESCRIPTION

       Clustal-Omega  is a general purpose multiple sequence alignment (MSA) program for proteins. It produces high quality MSAs and is capable of
       handling data-sets of hundreds of thousands of sequences in reasonable time.

       In default mode, users give a file of sequences to be aligned and these are clustered to produce a guide tree and this is used to  guide  a
       "progressive alignment" of the sequences.  There are also facilities for aligning existing alignments to each other, aligning a sequence to
       an alignment and for using a hidden Markov model (HMM) to help guide an alignment of new sequences that are  homologous	to  the  sequences
       used to make the HMM.  This latter procedure is referred to as "external profile alignment" or EPA.

       Clustal-Omega  uses  HMMs  for  the alignment engine, based on the HHalign package from Johannes Soeding [1]. Guide trees are made using an
       enhanced version of mBed [2] which can cluster very large numbers of sequences in O(N*log(N)) time. Multiple  alignment	then  proceeds	by
       aligning larger and larger alignments using HHalign, following the clustering given by the guide tree.

       In  its	current  form  Clustal-Omega can only align protein sequences but not DNA/RNA sequences. It is envisioned that DNA/RNA will become
       available in a future version.

USAGE

       Tool usage is available in /usr/share/doc/clustalo/README.

DEVELOPMENT

       Headers and libraries are available in libclustalo-dev package.

CITING

       Sievers F, Wilm A, Dineen DG, Gibson TJ, Karplus K, Li W, Lopez R, McWilliam H,
	Remmert M, Soding J, Thompson JD, Higgins DG (2011).  Fast, scalable generation of high-quality protein multiple sequence alignments
	using Clustal Omega. Mol Syst Biol 7.

AUTHOR

       Olivier Sallou (olivier.sallou (at) irisa.fr) - Man page and packaging

       Conway Institute UCD Dublin (clustalw (at) ucd.ie) - clustalo

version 1.0.3							 December 14, 2011						       clustalo(1)
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