BLAST BLAST Basic Local Alignment Search Tools similarity sequence sequence

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??????????????????????????????????????????-???????
????????????????????????

• ???
• ??. ????? ?????????
• ??????????????????????????? ?????????????????
  ????????????????????

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BLAST ??????? BLAST (Basic Local Alignment
Search Tools) ??????????????????????????????????
(similarity) ???????? (sequence)
??????????????????????????????????????
(???????????) ???????????????? ??? sequence ????
? ???????????????????????????????????? ????
?????????????????? ????????????? ???????
?????????????????????????????????? sequence
?????? Heuristic algorithm ???????????????????????
????? Local alignment ??????????? BLAST ??? 4
???????
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1. www BLAST ?????? web browser ???????????????
NCBI (National Center for Biotechnology
Information) ?????????????? BLAST
?????????????????????????????? BLAST
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2. Standalone BLAST ???????????????? BLAST
????????????????????????????? ????????????????????
?????????????????????????????? ???????????????????
?????????????????? ??????? NCBI
(ftp//ftp.ncbi.nlm.nih.gov/blast/db/)
?????????????????????? BLAST ??????
(ftp//ftp.ncbi.nlm.nih.gov/blast/executables)
??????????????????????????????????????????????????
?? ?????? Macintosh, Win32 (PC), LINUX, Solaris,
SGI, and HP UX systems
3. Network BLAST ???????????? NCBI ?????????
Blastcl3 ??????? BLAST network client
????????????????????????????????? BLAST server
??? NCBI ?????? TCP/PI protocol ??????? BLAST
???????????????? Blastcl3 ?????????????????????
ftp//ftp.ncbi.nlm.nih.gov/blast/network/netblast/
CURRENT/
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4. E-mail server ?????????????????????????????????
?????????????????????????????? world wide web -
?????????????????????????????????????????
(format) ???????? ????????????????????????????????
???????????????? blast_at_ncbi.nlm.nih.gov
??????????????????????????????????????????????
BLAST ?????? E-mail server ??????????????
blast_at_ncbi.nlm.nih.gov - ????????????????????
BLAST ???????????????????????????????????????
(Functional information) ?????????????????????????
???? (Evolutionary information) ????????????????
sequence ?????????????????? - BLAST ??? NCBI ???
BLAST ????????????????????????????????????????????
?? sequence ??????????????????? BLAST
???????????????????????????????? (homology)
?????????????????????????????????????
??????????????????????????????? sequence
??????????????????????????????????????????????????
???????????????
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?????????????????? BLAST
blastn ???????????????????????????????????????????
???????? (Nucleotide query sequence)
?????????????????????????????????????????
(NUCLEOTIDE database) blastp ???????????????????
protein query sequence ??????????????????????????(
???????????????)???????????????????? blastx
???????????????????????????????????????????????
(Translation) ????????????????????
??????????????????????????????????????????????????
?????????? ???????????????? 6 reading frames
(???????????????? 3 reading frames ??????
complementary strand ??? 3 reading frames)
????????????????????????????????? 6 frames
????????????????????????????????????????????? (
???????????TRANSLATED query - PROTEIN database )
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tblastn ??????????????????????????????????????????
??????????????????????????????????? 6 reading
frames ???????????????????????????????????????????
???? (PROTEIN query - TRANSLATED database)
tblastx ?????????????????????????????????????????
?????????????????????????????????????????????????
??????????????????????????????????????????????????
?????? 6 reading frames ??????????????????????????
????????????????????????? 6 reading frames
????????????????????????? (TRANSLATED query -
TRANSLATED database)
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blastn ?????????? BLAST ?????? sequence
???????????????????? ?????????????????????????????
???????????????? ???? Virus, Archea, Bacteria,
Eukaryote, plant, Fungi, Metazoa, Arthropod,
Vertebrate ??????? ???????????????????????????????
? (Scientific name) ????????????????????? ? ????
Arabidopsis thaliana, Bacillus subtilis,
Drosophila melanogaster, Escherichia coli, Homo
sapiens, HIV types 1 ???????
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FASTA format FASTA format ???????????????????????
??????????????????? (gt) ????????????????????????
1 ?????? ???????? FASTA definition line
??????????????????? sequence ?????????????????????
? 80 ??????? ???????????
gtgi532319pirTVFV2ETVFV2E envelope protein
ELRLRYCAPAGFALLKCNDADYDGFKTNCSNVSVVHCTNLMNTTVTTGL
LLNGSYSENRTQIWQKHRTSNDSALILLNKHYNLTVTCKRPGNKTVLPVT
IMAGLVFHSQKYNLRLRQAWCHFPSNWKGAWKEVKEEIVNLPKERYRGTN
DPKRIFFQRQWGDPETANLWFNCHGEFFYCKMDWFLNYLNNLTVDADHNE
CKNTSGTKSGNKRAPGPCVQRTYVACHIRSVIIWLETISKKTYAPPREGH
LECTSTVTGMTVELNYIPKNRTNVTLSPQIESIWAAELDRYKLVEITPIG
FAPTEVRRYTGGHERQKRVPFVXXXXXXXXXXXXXXXXXXXXXXVQSQHL
LAGILQQQKNLLAAVEAQQQMLKLTIWGVK
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????????????????????????????????????????????
solfware ???????????????????????
Web browser Netscape, navigator, Explorer,
Opera, Microsolf Internet ??? cut, copy ???
paste Search engine Yahoo, Lycos, InfoSeek,
HotBot, etc
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?????????????????????????????????????????
solfware ???????????????????????

• 1. ???????????????? nucleotide (reverse)
  ??????????????????? (complementary base)
• Genetic Computer Group Wisconsin Package-
• http//www.embl-heidelberg.de/toldo/Reverse.html
  
• 2. ?????????????????????????????????
  ????????????????????????????????? ????????????
  pI, MW ???????
• IMBG-
• http//www.mo.mahidol.ac.th/ResTools/biotools/bio
  tools11.html

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• 3. ????????????? DNA ????????????? (DNA
  translation) ????? possible reading frame ???????
  6 ??? ????????????????????????????????????????????
  ???????? 1 frame (???????????????????) ???
  program ??? Protein translation-
  http//expasy.ch/tools/dna.html
• 4. ??????????????????????? DNA ?????????????
  ??????????????????????????????????????????????????
  ??? ??? program ???Count codon program
• 5. Restriction map analysis ?????? program ???
  Webcutter- http//www.firstmarker.com/cutter/cut2
  .html

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• 6. Homology and similarity search
  ???????????????????? BLAST, FASTA ??? SSEARCH
• 7. Phylogenetic tree ?????????????????????????????
  ????? ???????????????????? Treebase (database),
  Dst, TreeGen, Phylip program ???????
• 8. Open Reading Frame ???? Coding region ??????
  program ??? ORF finder, FramePlot, DNA sequence
  translation, CDS ???????
• 9. Design primer
• 10. Protein structure

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??????????????? gene mutation ?????????
Mutation
Normal
Fasta format
Fasta format
Sequence alignment
Open reading frame
Open reading frame
Mutation site
Restiction site
Restiction site
Frimer Design