橡PNE記事補足

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1 UNIX --- MacOS X Linux --- MacOS X Darwin BSD UNIX Aqua Mac GUI graphical user interface MacOS UNIX IT WEB UNIX Mac Windows MacOS X UNIX OS UNIX 1

2 2 MacOS9 Windows98 (Me) Windows 2000 (NT) Windows PC-UNIX GUI OS OS 30 MB CD 3D 3D DVD GUI OS UNIX UNIX UNIX LAN Mac

3 3 Windows UNIX Mac Windows UNIX UNIX PC-UNIX PC-UNIX FTP FTP WEB PC-UNIX PC-UNIX PC-UNIX UNIX OS Linux OS Linux Windows dual boot OS OS Linux Windows LAN VMware Linux Windows Mac OS X

4 BSD Darwin OS Mac UNIX Mac Windows Mac OS X Mac OS Mac OS 9 Terminal UNIX Mac Samba Windows Mac Mac MacOS X Mac Linux MacOS X MacOS X G3 G4 Mac imac PowerMac G4 CPU 1 GB MacOSX GUI 500 MHz 700 MHz PowerMac G4 1 GB 60 GB HD ethernet MacOS X postscript MacOS X Apple Store HD MacOS9.1 X OS CD 4

5 CD root su root Internet Explorer 5 IE5 ftp NetInfo Manager System Preferences Mac UNIX MacOS X Mac CPU 80% 95% Mac UNIX >console MacOSX version 10.1 UNIX >console UNIX ls someone /Users/someone ls al Mac X logout X (1) X UNIX Mac Windows UNIX 5

6 X UNIX Netscape Darwin X MacOS X IE 5 Netscape X XFree86 OSX GNU MacOSX URL MacOS X 10.1 Quartz (Xquartz.tgz ) MacOSX Terminal ( cd <directory> ) sh Xinstall.sh X XDarwin XDarwin --> XDarwin X.xmodmaprc HP XDarwin UNIX X keycode keysym X Mac UNIX twm LessTif mwm X X X GUI UNIX Mac A X twm MacOSX 6

7 Pager X >console startx X Mac exit logout X /usr/x11r6 /Applications/XDarwin /usr UNIX MacOSX Finder Terminal Finder Linux LessTif openmotif (3) Clustal X Motif (LessTif) NCBI toolbox (blast ) (2) LessTif Motif openmotif lesstif openmotif MacOSX lesstif Darwin OS Terminal tar.gz gzip (gzip -d ) tar (tar xvf tar ) UNIX 7

8 Courier gzip tar MacOS X tar tar zxvf UNIX ( cd )./configure make make install /usr/local/lesstif 200 Mb HD configure configure Darwin config.sub config.guess /usr/libexec/ cp /usr/libexec/config.sub. cp GNU./configure configure -enable-static Motif enable-build-20 enablebuild-12./configure help configure make clean make distclean make install /usr/local/lesstif /usr/x11r6 /usr/x11r6/lib /usr/x11r6/include su root ln s /usr/local/lesstif/motif2.0/lib/libxm.a /usr/x11r6/lib ln s /usr/local/lesstif/motif2.0/include/xm /usr/x11r6/include/ root, exit (3) NCBI toolbox 8

9 NCBI toolbox GenomeNet NCBI FTP ncbi.tar.gz MacOS X /usr/local/ someone /Users/someone /usr/local ncbi ncbi make makeall.unx TextEdit VIBLIBS= VIBFLAGS= VIBLIBS= -L/usr/X11R6/lib lxm lxpm lxmu lxp lxt lx11 lxext VIBFLAGS= -I/usr/X11R6/include I/usr/local/LessTif/Motif2.0/include - DWIN_MOTIF ncbi platform darwin.ncbi.mk NCBI toolbox # NCBI = # NCBI_BIN_MASTER = /usr/local/ncbi/bin NCBI_BIN_COPY = /usr/local/ncbi/bin NCBI_INCDIR = /usr/local/ncbi/include NCBI_LIBDIR = /usr/local/ncbi/lib NCBI_ALTLIB = /usr/local/ncbi/altlib ncbi ncbi ncbi/make/makedis.csh & tee out.makedis.csh ncbi make makedis.csh C out.makedis.csh & tee ncbi build ls blastall, ls formatdb 9

10 build rm f * build ncbi csh rm f *.c *.h make* -f *.h * ncbi/lib rm f *.a -f blastall BLAST formatdb mv blast* formatdb../bin ncbi/bin ncbi/bin /usr/local/bin ncbi /usr/local.tcshrc set path = ( $path /usr/local/ncbi/bin ) ln s /usr/local/ncbi/bin/blastall /usr/local/bin/blastall /usr/local/bin cp /usr/local/ncbi/bin/blastall /usr/local/bin /usr/local/ncbi/lib NCBI.ncbirc /usr/local/ncbi NCBI.tcshrc setenv NCBI /usr/local/ncbi (4) Clustal X Clustal X (/usr/local/clustal ) Linux clustalx1.81 Terminal clustal makefile vi LessTif, ncbi CC = cc MacOS X cc 10

11 NCBI_INC = /usr/local/ncbi/include NCBI_LIB = /usr/local/ncbi/lib LXFLAGS = -L$(NCBI_LIB) lvibrant lncbi -L/usr/X11R6/lib lxm lxmu lxt lx11 -lsm lice -l /usr/x11r6/lib libxm.a -lxm -L MacOS X -lm C make clustalx MacOSX file clustalx clustalw clustalx /usr/local/bin makefile /usr/local/bin UNIX rehash exit X clustalx Clustal X MacOS X Terminal njplot clustalx makefile Linux XDarwin UNIX Perl, Tcl/Tk MacOS X Perl Tcl Tk wish Mac GUI MacOS X Tk X Aqua Tk 11

12 Tcl/Tk Tcl Tk Tk Tcl /usr/local/ SISEQ, Phylip fastdnaml, Molphy FASTA, HMM X MacOS Terminal make (/usr/local/bin) SISEQ Mac Windows UNIX GUI Tk SRS URL Genome Net KEGG DNA GenBank, EMBL, SwissProt, PIR GenBank EMBL SwissProt PIR GenBank SwissProt, PIR, Pfam, Prodom SRS SISEQ SRS 12

13 GenBank nt, nr (nonredundant nucleotide, protein) swissprot, ORF genpept EST est_human, est_others NCBI GenomeNet FTP mget ftp Z gz uncompress, gzip d HD NCBI toolbox formatdb Blast -i DNA -pf formatdb.log DNA N X BLAST BLASTDB Linux MacOS X C TC setenv BLASTDB /usr/local/db blastall -i -d -p -o formatdb i blastall i test.seq d nr p blastp o test.results test.seq FASTA 13

14 UNIX MacOS X MacOS X Finder Terminal Terminal vi TextEdit rtf /Developer Simple Text Linux MacOS X Darwin OS BSD UNIX MacOS X GNU gcc UNIX /etc NetInfo Magager MacOS X Mac Darwin Appleshare Mac X Mac G4 BLAST Windows Linux MacOS X UNIX MacOS X 14

15 1. Thompson, J.D., Higgins, D.G. and Gibson, T.J.: Nucl. Acids Res. 22, (1994) Clustal W 2. Felsenstein, J.: Annu. Rev. Genet. 22, (1988) Phylip 3. Sato, N.: Bioinformatics 16, (2000) 4. Baxevanis, A. D.: Nucleic Acids Res. 29, 1-10 (2001) 5. Altschul, S. F., Madden, T. L., Schäffer, A. A., Zhang, J., Zhang, Z., Miller, W. and Lipman, D. J.: Nucleic Acids Res. 25, (1997) -- Gapped BLAST 6. Zhang, Z., Schäffer, A. A., Miller, W., Madden, T. L., Lipman, D. J., Koonin, E. V. and Altschul, S. F.: Nucleic Acids Res. 26, (1998) PSI BLAST 15

16 URL 1. Apple 2. MacOS X GNU 3. Linux 4. XFree Sato 6. LessTif 7. NCBI toolbox ftp://ftp.genome.ad.jp/pub/db/ncbi/toolbox/ncbi tools/ncbi.tar.gz 8. Clustal X ftp://ftp-igbmc.u-strasbg.fr/pub/clustalx/ 9. Njplot ftp://pbil.univ-lyon1.fr/software/njplot.html 10. Phylip FASTA ftp://ftp.virginia.edu/pub/fasta/ 12. List of free software in molecular biology Molecular Linux linux/ 14. GenBank ftp://ftp.genome.ad.jp/pub/db/ncbi/genbank/ ftp://ftp.genome.ad.jp/pub/db/ncbi/blast/db/ (nr, nt, swissprot ) 15. EMBL ftp://ftp.genome.ad.jp/pub/db/ebi/embl/release/ 16. SwissProt ftp://ftp.genome.ad.jp/pub/db/ebi/swissprot/release/ 17. Pfam ftp://ftp.genome.ad.jp/pub/db/ebi/pfam/ 18. SRS Mozilla 16

17 ls HP 1..xmodmaprc (Xfree86 ) 2..tcshrc ( ) 3. darwin.ncbi.mk (/usr/local/ncbi/platform/) 4. makeall.unx (/usr/local/ncbi/make/) 5..ncbirc (/usr/local/ncbi/) 6. makefile (ClustalX) 17

18 ls ls al cd pwd cp rm mv gzip d tar xvf make configure DOS rename UNIX gz tar README INSTALL 18

19 . command./command DOS.. tonari cd../tonari 19

KNOB Knoppix for Bio Itoshi NIKAIDO

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橡PNE記事補足

橡PNE記事補足