1. Sequence alignment
    Muscle　( http://www.ebi.ac.uk/Tools/msa/muscle/ )~Web上で入力
    Clustal omega ( http://www.ebi.ac.uk/Tools/msa/clustalo/ )~Web上で入力
    MAFFT ( http://mafft.cbrc.jp/alignment/software/ )~パソコン上で使用

    　

  2. 蛋白質の機能を調べる
    i) Uniprot ( http://www.uniprot.org/ )
    ii) アミノ酸配列のドメイン解析 (see Mamada's Dev Biol paper for references):
    SignalP ( http://www.cbs.dtu.dk/services/SignalP/ )
    SMART ( http://smart.embl-heidelberg.de/ )
    TMHMM ( http://www.cbs.dtu.dk/services/TMHMM/ )
    Pfam ( http://www.sanger.ac.uk/Software/Pfam/ )
    NCBI conserved domain database ( http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml )

  3. To access the Xenopus tropicalis genemic sequence database:
    http://genome.jgi-psf.org/Xentr4/Xentr4.home.html

  4. To blast search against Xenopus EST sequences
    NBRP Xenopus http://shigen.nig.ac.jp/xenopus/blast.jsp;jsessionid=B2FAFE4BA1C90F6AD4B015460EEECFC7

  5. To design PCR primer sets or sequencing primers:
    Primer3Plus: Primer3Plus Version, 2.4.0; Primer3 Version, libprimer3 release 2.3.6
    http://primer3plus.com/cgi-bin/dev/primer3plus.cgi
    ( http://primer3.sourceforge.net/webif.php )

  6. To calculate Tm for oligo sequences, etc.：
    http://www.basic.northwestern.edu/biotools/oligocalc.html
    http://mbcf.dfci.harvard.edu/docs/oligocalc.html
    http://www.promega.com/techserv/tools/biomath/calc11.htm
    ( http://www.promega.com/biomath/ )
    hairpinなどのチェック：http://sg.idtdna.com/calc/analyzer

  7. Cleavage Close to the End of DNA Fragments:
    https://www.neb.com/tools-and-resources/usage-guidelines/cleavage-close-to-the-end-of-dna-fragments
    https://www.neb.com/~/media/NebUs/Files/Chart%20image/cleavage_olignucleotides_old.pdf

  8. To find codon usage in Xenopus：
    http://www.kazusa.or.jp/codon/cgi-bin/showcodon.cgi?species=8355
    ( http://www.kazusa.or.jp/codon/ )

  9. To search DNA database with keywords, accession numbers, etc.：
    http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Nucleotide

  10. To search protein database with keywords, accession numbers, etc.：
    http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Protein

  11. To perform blast search,：
    http://blast.ncbi.nlm.nih.gov/Blast.cgi

  12. To submit DNA sequences to DDBJ/Genebank database in Japan：
    http://sakura.ddbj.nig.ac.jp/top-j.html

  13. To contact the Xenopus Community in Japan:
    http://www.ipc.shizuoka.ac.jp/~ehkurod/xcij/
    http://www.biol.s.u-tokyo.ac.jp/users/xcij/xcij.html

  14. About GCG, the Wisconsin Package：
    http://www.yk.rim.or.jp/~aisoai/ResTools/biotools/biotools13.html

  15. To find the number of EST sequences in each organism：
    http://www.ncbi.nlm.nih.gov/dbEST/dbEST_summary.html

  16. To obtain some vector sequences (lambda-FIX II etc.): ：
    http://www.stratagene.com/vectors/selection/lambda.htm

  17. Sakura DDBJ登録における、各Feature、Qualifierの定義
    Feature keyの定義　　 http://www.ddbj.nig.ac.jp/sub/ref5-j.html
    Qualifier key の定義　 http://www.ddbj.nig.ac.jp/sub/ref6-j.html
    Organism Qualifier について http://www.ddbj.nig.ac.jp/sub/ref8-j.html
    CDS feature について http://www.ddbj.nig.ac.jp/sub/cds-j.html
    登録の見本　 http://www.ddbj.nig.ac.jp/sub/example-j.html

  18. 種間の進化距離　"Time Tree"
    http://www.timetree.org/time_e_query.php?taxon_a=Danio%20rerio&taxon_b=Oryzias%20latipes

  19. TIGR EST similarity search
    http://compbio.dfci.harvard.edu/tgi/cgi-bin/tgi/Blast/index.cgi


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