Gene mapping - linkage and association: topic

This is a public forum

Join this group to post on this forum

Regarding computing speed of linkage programs.

S.Rekha Reddy

Saturday, 07 Jul 2007 05:49 UTC

hi to all..

I m working on Human Genetics. I need to calculate LOD scores(using MLINK) for a family of around 50 individuals with 3 loops. It takes atleast 6-7 hrs to calculate for each marker.
1. Can anyone tell me how to increase the computing speed?
2. Can u suggest me good haplotyping programs for two point mapping?

Thanks in advance

  • Replies

    Post a reply

    • Barbara Kremeyer

      07 Jul 2007 | 13:27

      Hi there,

      I am not too sure about how to increase the computing speed for your LOD score calculation. Do you have access to a faster computer? Or maybe a server where the calculations can run in the background? Do you know about the Litbio service in Italy for which you can register (it’s free but takes some time to get registered)? They provide access to FASTLINK which personally I have never used, but it is a faster version of the LINKAGE package. So maybe that could help?
      As for a haplotyping programme, I have only used Simwalk2 so far but found it very good.
      I hope that helps a bit!

    • S.Rekha Reddy

      08 Jul 2007 | 12:43

      hi.. thanks for ur reply.
      i don ve access to faster computer. I m using Pentium III. I never heard about that Litbio. let me try that. can i use Simwalk2 for calculating 2-point mapping? or is that for multi-point mapping? what about recombination errors and missing genotypes in Simwalk2? how does that affect?

    • Barbara Kremeyer

      10 Jul 2007 | 08:06

      Hi,

      as for LOD score calculation, Simwalk2 does multipoint mapping, not two-point. But the haplotyping option should do as many markers as you specify – the minimum would be two. (You were asking for a haplotyping programme, right?)

    • Lorna Houlihan

      16 Jul 2007 | 12:45

      Hello,
      I have 2 suggestions that might help. The first one is to split the family, use a program like Mlink/Merlin and add your LOD scores. Otherwise you could try an online program called “Superlink” that works well for large families.
      Good luck,
      Lorna

    • Barbara Kremeyer

      16 Jul 2007 | 12:54

      Hi Lorna,

      that Superlink programme sounds good – I haven’t heard of it before. Could you maybe post a link to it? Many thanks!

      Barbara

    • Lorna Houlihan

      16 Jul 2007 | 13:03

      Here you go
      splitting families
      merlin
      superlink
      Sorry, I should of sent these with the earlier message.
      Lorna

    • Barbara Kremeyer

      17 Jul 2007 | 07:19

      Thanks! :-)

    • S.Rekha Reddy

      23 Jul 2007 | 08:47

      hi !!

      canu plz tell me the difference betwwen fastlink and linkage program? i aware that fastlink is updated version of linkage. Is tat input file(like pre file, ped file n dat file) varies from linkage?

    • S.Rekha Reddy

      23 Jul 2007 | 08:52

      hi..
      can u plz tell me the difference between fastlink and linkage program? i m aware that fastlink is updated version of linkage. Is tat input file(like pre file, ped file n dat file) varies from linkage?

    • Mark Silberstein

      30 Jul 2007 | 05:10

      You may want to try Superlink-online:
      http://bioinfo.cs.technion.ac.il/superlink-online.

      It is exactly what you need – LOD scores for very large pedigrees, but rather small amount of markers.

      Its power comes from the use of several thousands of computers worldwide for parallel execution of the computation…

      Feel free to ask any questions.

      Mark

    Post a reply
Search forums Advanced search

Submit this topic to

web feed

Advertisement