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HMMer

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HMMer → profile HMMs for protein sequence analysis  HMMer은 hidden markov models을 적용한 수학적인 방법을 기초로하여 개발된것으로,  모든 염기 서열을 인지한 후 multiple alignment를 통해 비교 가능한 염기 서열을 찾아낸다.  관련문서 : <a href="http://hmmer.wustl.edu/#overview">http://hmmer.wustl.edu/#overview</a> <~~font size="3"~~strong>관련소프트웨어: <a href="http://www.clcbio.com/index.php?id=971">http://www.clcbio.com/index.php?id=971</a><a href="http://hmmer.wustl.edu/#overview"></a> =============================================================================~~=======~~ Download : <a href="http://hmmer.wustl.edu/#download">http://hmmer.wustl.edu/#download</a> <dt> Source code version </dt><dd>Download: <a href="ftp://ftp.genetics.wustl.edu/pub/eddy/hmmer/2.3.2/hmmer-2.3.2.tar.gz">hmmer-2.3.2.tar.gz</a> </dd><dt>AMD Opteron/Linux </dt><dd>Download: <a href="ftp://ftp.genetics.wustl.edu/pub/eddy/hmmer/2.3.2/hmmer-2.3.2.bin.amd-opteron-64-suse-linux.tar.gz">hmmer-2.3.2.bin.amd-opteron-64-suse-linux.tar.gz</a> Opteron 242, 2x1.6 GHz; SUSE Linux; GCC 3.3.3; --enable-threads --enable-lfs [Contributed by Martin Gollery, University of Nevada, Reno.] RPMs built with the <a href="http://www.pgroup.com/">Portland Group</a> C compiler are also available from Joe Landman and <a href="http://www.scalableinformatics.com/">Scalable Informatics, LLC</a>: you can download <a href="http://downloads.scalableinformatics.com/downloads/hmmer/hmmer-2.3.2-5pgi.x86_64_pgi.rpm">hmmer-2.3.2-5pgi.x86_64_pgi.rpm</a> from their site. </dd><dt>Apple Macintosh PowerPC OS/X </dt><dd>Download: <a href="ftp://ftp.genetics.wustl.edu/pub/eddy/hmmer/2.3.2/hmmer-2.3.2.bin.powerpc-apple-osx.tar.gz">hmmer-2.3.2.bin.powerpc-apple-osx.tar.gz</a> Apple PowerPC; 2x G4/1.25Ghz; OS/X Darwin 6.8; --enable-threads --enable-lfs --enable-altivec; CFLAGS="-O" Includes Altivec optimizations contributed by Erik Lindahl, Stanford University. </dd><dt>Compaq Alpha Tru64 </dt><dd>Download: <a href="ftp://ftp.genetics.wustl.edu/pub/eddy/hmmer/2.3.2/hmmer-2.3.2.bin.alpha-tru64.tar.gz">hmmer-2.3.2.bin.alpha-tru64.tar.gz</a> Compaq Alpha ES40; Tru64 5.1B; --enable-threads --enable-lfs; CC=cc CFLAGS=-O </dd><dt>Compaq Alpha Linux </dt><dd>Download: <a href="ftp://ftp.genetics.wustl.edu/pub/eddy/hmmer/2.3.2/hmmer-2.3.2.bin.alpha-linux.tar.gz">hmmer-2.3.2.bin.alpha-linux.tar.gz</a> Compaq Alpha ES40; Red Hat Alpha Linux 7.1; --enable-threads --enable-lfs; CFLAGS=-O ~~~~</dd><dt>Hewlett/Packard IA64 (Itanium2), Linux </dt><dd>Download: <a href="ftp://ftp.genetics.wustl.edu/pub/eddy/hmmer/2.3.2/hmmer-2.3.2.bin.ia64-hp-linux.tar.gz">hmmer-2.3.2.bin.ia64-hp-linux.tar.gz</a> HP rx2600; 2xItanium2/900/1.5; Linux 2.4.18-e.12; --enable-threads --enable-lfs; CFLAGS="-O2" </dd><dt>Hewlett/Packard IA64 (Itanium2), HP/UX </dt><dd>Download: <a href="ftp://ftp.genetics.wustl.edu/pub/eddy/hmmer/2.3.2/hmmer-2.3.2.bin.ia64-hp-hpux.tar.gz">hmmer-2.3.2.bin.ia64-hp-hpux.tar.gz</a> HP rx2600; 2xItanium2/900/1.5; HP/UX 11.22; --enable-threads --enable-lfs; CC=cc CFLAGS="-O"

</dd><dt>~~IBM Power4~~Hewlett/Packard IA64 (Itanium2), Linux </dt><dd>Download: <a href="ftp://ftp.genetics.wustl.edu/pub/eddy/hmmer/2.3.2/hmmer-2.3.2.bin.~~ibm-pwr4~~ia64-~~suse~~hp-linux.tar.gz">hmmer-2.3.2.bin.~~ibm~~ia64-~~pwr4-suse~~hp-linux.tar.gz</a> ~~IBM pSeries~~HP rx2600; ~~Power4~~2xItanium2/900/1.5; ~~SusE~~ Linux ~~8 (SLES8)~~2.4.18-e.12; --enable-threads --enable-lfs; ~~CC=xlc_r~~ CFLAGS="-O O2" </dd><dt>Hewlett/Packard IA64 (Itanium2), HP/UX </dt><dd>Download: <a href="ftp://ftp.genetics.wustl.edu/pub/eddy/hmmer/2.3.2/hmmer-2.3.2.bin.ia64-~~q64~~ hp-~~qtune~~hpux.tar.gz">hmmer-2.3.2.bin.ia64-~~qcache=auto"~~hp-hpux.tar.gz</a> ~~[Provided by Bob Arenburg and IBM Life Sciences~~HP rx2600; 2xItanium2/900/1.] 5; HP/UX 11.22; --enable-threads --enable-lfs; CC=cc CFLAGS="-O"

</dd><dt>IBM Power4, ~~AIX~~Linux </dt><dd>Download: <a href="ftp://ftp.genetics.wustl.edu/pub/eddy/hmmer/2.3.2/hmmer-2.3.2.bin.ibm-~~aix~~pwr4-suse-linux.tar.gz">hmmer-2.3.2.bin.ibm-~~aix~~pwr4-suse-linux.tar.gz</a> IBM pSeries ~~630~~; ~~4xPower4/1.2GHz~~Power4; ~~AIX 5.2~~SusE Linux 8 (SLES8); --enable-threads --enable-lfs; CC=xlc_r CFLAGS="-~~O2&~~O -q64 -qtune=pwr4 -qcache=auto" ~~On large multiprocessor systems (8 cpus or more), you want to add &quot~~[Provided by Bob Arenburg and IBM Life Sciences.]  ~~-bmaxdata:0x80000000" to CFLAGS and recompile to enable AIX's "Large Program Support"; otherwise~~</dd><dt>IBM Power4, AIX ~~only allows a program to allocate 256 MB of RAM by default. </font~~ </dt><~~br /~~dd>Download: </~~dd><dt>Intel FreeBSD<~~ftp.genetics.wustl.edu/pub/eddy/~~strong> <~~hmmer/~~dt><dd>Download: <a href="ftp://ftp.genetics.wustl.edu/pub/eddy/hmmer/2.~~2.3.2/hmmer-2.3.2.bin.~~intel~~ibm-~~freebsd~~aix.tar.gz">hmmer-2.3.2.bin.~~intel~~ibm-~~freebsd~~aix.tar.gz</a> ~~Dell 1550/VMWare~~IBM pSeries 630; ~~2xPIII~~4xPower4/1.~~27/512K~~2GHz; ~~FreeBSD 4~~AIX 5.72; --enable-threads --enable-lfs; CC=xlc_r CFLAGS="-O2 ~~-static&~~" ~~~~ ~~ </dd><dt>Intel GNU/Linux </dt><dd>Download~~On large multiprocessor systems (8 cpus or more), you want to add "-bmaxdata: <0x80000000" to CFLAGS and recompile to enable AIX's "Large Program Support"; otherwise, AIX only allows a ~~href="ftp://ftp~~program to allocate 256 MB of RAM by default.~~genetics.wustl.edu~~</~~pub~~font> </~~2.3.2~~dd><dt>Intel FreeBSD</~~hmmer-2.3.2.bin.intel-linux.tar.gz"~~strong> </dt><dd>Download: <~~font color~~a href="~~#000000">~~ftp://ftp.genetics.wustl.edu/pub/eddy/hmmer/2.3.2/hmmer-2.3.2.bin.intel-~~linux~~freebsd.tar.gz">color="#000000">hmmer-2.3.2.bin.intel-freebsd.tar.gz</a> ~~Or, as an RPM: <a href~~Dell 1550/VMWare; 2xPIII/~~ftp~~1.~~genetics.wustl~~27/512K; FreeBSD 4.~~edu/pub/eddy/hmmer/2.3.2/hmmer~~7; --~~2.3.2~~enable-~~1static_pvm.i686.rpm">hmmer~~"-~~2.3.2~~O2 -~~1static_pvm.i686.rpm~~static" <~~font size="-1"~~/dd>~~Dell 6450; 4xPIII~~<dt>Intel GNU/~~700~~Linux </~~2; Red Hat Linux 7.2; --enable-threads --enable-lfs --enable-pvm; CC~~dt><dd>Download: <a href=~~icc CFLAGS="-O3 -axMKW -static" <br~~ "ftp://ftp.genetics.wustl.edu/pub/eddy/hmmer/~~>the RPM spec file is available: <a href="ftp://ftp~~2.~~genetics~~3.~~wustl.edu/pub/eddy~~2/hmmer/-2.3.2~~/hmmer~~.bin.intel-~~pvm~~linux.tar.~~spec~~gz">hmmer-~~pvm~~2.3.2.bin.intel-linux.tar.~~spec~~gz</a> Or, as an RPM: <br~~ ftp.genetics.wustl.edu/><pub/~~dd><dt>Intel OpenBSD<~~eddy/hmmer/~~strong> <~~2.3.2/~~dt><dd>Download: <a href="ftp://ftp~~hmmer-2.3.~~genetics.wustl.edu/pub/eddy/hmmer/~~2-1static_pvm.3i686.~~2/hmmer-2.3.2.bin.intel-openbsd.tar.gz~~rpm">hmmer-2.3.2~~.bin.intel~~-~~openbsd~~1static_pvm.~~tar~~i686.gzrpm</a> Dell ~~1550/VMWare~~6450; ~~2xPIII~~4xPIII/~~1.27~~700/~~512K~~2; ~~OpenBSD 3~~Red Hat Linux 7.2; --enable-threads --enable-lfs--enable-pvm; CC=icc CFLAGS="-O2 O3 -axMKW -static" ~~~~ the RPM spec file is available: </~~dd><dt>Intel Solaris<~~ftp.genetics.wustl.edu/pub/eddy/hmmer/~~strong> <~~2.3.2/~~dt><dd~~hmmer-pvm.spec">~~Download:~~ <~~a href~~font color="~~ftp:~~#000000">hmmer-pvm.spec</~~ftp.genetics.wustl.edu~~a> </~~pub~~font> </~~2.3.2~~dd><dt>Intel OpenBSD</~~hmmer-2.3.2.bin.intel-solaris.tar.gz"~~strong><~~font color~~/dt><dd>Download: <a href="~~#000000">hmmer-2~~ftp://ftp.3genetics.~~2.bin~~wustl.edu/pub/eddy/hmmer/2.3.2/hmmer-2.3.2.bin.intel-~~solaris~~openbsd.tar.gz">color="#000000">hmmer-2.3.2.bin.intel-openbsd.tar.gz</a> Dell 1550/VMWare; 2xPIII/1.27/512K; ~~x86 Solaris 9~~OpenBSD 3.2; --enable-threads --enable-lfs; CFLAGS="-O2-static" </dd><dt>~~Silicon Graphics IA64 (Itanium2), Linux~~Intel Solaris </dt><dd>Download: <a href="ftp://ftp.genetics.wustl.edu/pub/eddy/hmmer/2.3.2/hmmer-2.3.2.bin.~~ia64~~intel-~~sgi-linux~~solaris.tar.gz">hmmer-2.3.2.bin.~~ia64~~intel-~~sgi-linux.~~solaris.tar.gz</a> ~~Silicon Graphics Altix 3000~~Dell 1550/VMWare; ~~16xItanium2/900~~2xPIII/1.527/512K; ~~Linux 2.4.19~~x86 Solaris 9; --enable-threads --enable-lfs; CFLAGS="-O2 ~~-static&~~" </dd><dt>Silicon Graphics ~~MIPS IRIX~~IA64 (Itanium2), Linux </dt><dd>Download: <a href="ftp://ftp.genetics.wustl.edu/pub/eddy/hmmer/2.3.2/hmmer-2.3.2.bin.ia64-sgi-~~irix64~~linux.tar.gz">hmmer-2.3.2.bin.ia64-sgi-~~irix64~~linux.tar.gz</a> Silicon Graphics ~~Origin200~~Altix 3000; ~~4xMIPS R10K~~16xItanium2/~~180,195~~900/1.5; Linux 2~~; IRIX 6~~.54.1219; --enable-threads --enable-lfs; CFLAGS="-O2 -static" </dd><dt>~~Sun Sparc Solaris~~Silicon Graphics MIPS IRIX </dt><dd>~~[The Solaris box in our compile farm has recently decided to quit, after years of faithful service. For now, build from the <a href~~Download: <a href="ftp://ftp.genetics.wustl.edu/pub/eddy/hmmer/2.3.2/hmmer-2.3.2.~~tar~~bin.gzsgi-irix64.tar.gz">~~source release~~hmmer-2.3.2.bin.sgi-irix64.tar.gz</a> ~~instead. We have one report that~~ Silicon Graphics Origin200; 4xMIPS R10K/180,195/2; IRIX 6.35.~~2 does not compile cleanly on Solaris 8: you may need to manually add~~ 12; --enable-threads -~~lnsl to LIBS in src~~-enable-lfs; CFLAGS="-O2 -static" </~~Makefile, after running .~~font> <~~strong~~/dd><~~font size="3"~~dt>Sun Sparc Solaris</dt><dd>[The Solaris box in our compile farm has recently decided to quit, after years of faithful service. For now, build from the <a href="ftp://ftp.genetics.wustl.edu/pub/eddy/hmmer/2.3.2/hmmer-2.3.2.tar.gz">source release</~~strong~~a>~~<br instead. We have one report that 2.3.2 does not compile cleanly on Solaris 8: you may need to manually add -lnsl to LIBS in src/Makefile, after running ./configure. We will resolve this in a subsequent release, as soon as we have access to Solaris again.]  ============================================================================= <div class="printfooter">원본 주소 - '<a href="http://biocc.ngic.re.kr/Biopedia/Biowiki/index.php/HMMer">http://biocc.ngic.re.kr/Biopedia/Biowiki/index.php/HMMer</a>'</div></dd>

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