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  • How to count the repeating times of a certain 11bp long sequence

    Hi, all
    I want to count the repeating times of an 11bp long sequence(for example: tcgtgacggta ) in human and mouse genome. Further I need know the positions of this sequence located in. This 11bp sequence is a potential motif . First I need know how many copies of this sequence in human and moue genomes. And then to know where they are.

    Is there any tool for this?

    Thanks .

  • #2
    Hi HSV-1,

    You can use bowtie with option -c TCGTGACGGTA
    and specify that you want to output all alignments via option -a.
    However, in this case you also need to specify that only perfect matches are allowed via -v 0.

    See http://bowtie-bio.sourceforge.net/manual.shtml for more details.

    Regards
    Last edited by rboettcher; 02-05-2013, 07:48 AM.

    Comment


    • #3
      Here's a fast C solution ... output is 0 based (so add one).

      This takes about 2 minutes on my 2000 bogomips machine for hg19 ...

      ______ begin code _______
      // this program finds short patterns and reverse complemented patterns in *.fa fasta (genome) files
      // how to compile: gcc -Wall -O3 -o patmatch patmach.c
      // how to use : for i in *.fa; do cat $i | ./patmatch; done

      #include <stdio.h>
      #include <string.h>
      #include <stdlib.h>
      #include <ctype.h>

      // put your pattern in pat1 and the reverse complement in pat2 ...
      char pat1[] = "TCGTGACGGTA"; // use upper case - NB: this should be a parameter but you can do it
      char pat2[] = "TACCGTCACGA"; // reverse complement of pat1

      #define MAXCHROMSIZE 254235640 // maximum chromsome size - edit as necessary - you will need to fix this IF you're using a whole genome FASTA
      char chr[MAXCHROMSIZE + 50];

      int main()
      {
      long int i,len;
      int j;
      char header[5012];
      char s[5012];
      char *spot = &chr[0];

      memset(chr,0,sizeof(chr));
      while (gets(s))
      {
      if (s[0] == '>') { strcpy (header,s); continue;}
      for (i=0;s[i];i++) s[i] = toupper(s[i]);
      strcat(spot,s);
      for ( ; *spot ; spot++) ;
      }
      len = spot-chr;
      spot = chr;
      for (i=0;i<len;i++)
      {
      if (chr[i] == (char)0) break;
      for (j=0;pat1[j]==chr[i+j];j++);
      if (j == 11) printf("F %s at %ld\n",header,i);
      for (j=0;pat2[j]==chr[i+j];j++);
      if (j == 11) printf("R %s at %ld\n",header,i);
      }
      return 0;
      }

      _______ end code ______

      Example for hg19 fastas ...

      -bash-3.00$ for i in *.fa; do cat $i | ./patmatch; done
      R >chr10 at 111870831
      F >chr11 at 36061863
      R >chr11 at 77190239
      R >chr12 at 119747880
      R >chr14 at 81206117
      R >chr14 at 95419269
      R >chr16 at 11844841
      F >chr16 at 78553508
      R >chr17 at 45266108
      F >chr1 at 17428420
      F >chr1 at 52442586
      F >chr2 at 25065131
      R >chr2 at 53867779
      R >chr2 at 114616666
      F >chr3 at 55121176
      F >chr4 at 1412897
      R >chr4 at 136465390
      R >chr5 at 84661141
      R >chr5 at 103058499
      F >chr7 at 2875412
      R >chr9 at 75467056
      Last edited by Richard Finney; 02-05-2013, 11:28 AM.

      Comment


      • #4
        This can be done with Biopieces (www.biopieces.org) like this:

        Code:
        read_fasta -i genome.fna | patscan_seq -p tcgtgacggta | write_bed -o out.bed -x

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