MultipleAlignment 프로그램.

• http://www.ebi.ac.uk/clustalw/ (웹서비스)

• http://bimas.dcrt.nih.gov/clustalw/clustalw.html (관련 페이퍼)

관련정보

• Program server in KRIBB : http://plant.pdrc.re.kr/gene/align/clustalW.html

• OperatingSystem별 다운로드 : ftp://ftp-igbmc.u-strasbg.fr/pub/ClustalX/

• BioPython에서 사용하기 : [BioPythonTutorial/CookBook/Alignment]

Standalone manual

Sequence Input From Disc

모든 입력서열은 하나의 파일내에 존재해야한다. 다음의 7가지 서열포맷을 자동인식한다.

• NBRF-PIR

• EMBL-SwissProt

• FastaFormat (Pearson)

• Clustal (*.aln)

• GCG-MSF (Pileup)

• GCG9-RSF

• GDE flat file

Multiple Alignments

입력서열에 대해 MultipleAlignment를 실행한다. 세부메뉴가 있다.

1. Do complete multiple alignment now (Slow/Accurate)
2. Produce guide tree file only
3. Do alignment using old guide tree file
4. Toogle Slow/Fast pairwise alignments = SLOW

5. PairwiseAlignment parameters

   • Slow/Accurate alignments
     1. Gap open penalty : 10.00
     2. Gap extension penalty : 0.10
     3. Protein weight matrix : Gonnet series
     4. DNA weight matrix : IUB
   • Fast/Approximate alignments
     1. Gap penalty : 3
     2. K-tuple (word) size : 1
     3. No. of top diagonals : 5
     4. Window size : 5
   • Toggle Slow/Fast pairwise alignments = SLOW

6. MultipleAlignment parameters

   1. Gap open penalty : 10.00
   2. Gap extension penalty : 0.20
   3. Delay divergent sequences : 30%
   4. DNA transitions weight : 0.50
   5. Protein weight matrix : Gonnet series
   6. DNA weight matrix : IUB
   7. Use negative matrix : OFF
   8. Protein Gap Parameters
      1. Toggle Residue-specific penalties : ON
      2. Toggle Hydrophilic penalties : ON
      3. Hydrophilic residues : GPSNDZEKR
      4. Gap separation distance : 4
      5. Toggle end gap separation : OFF
7. Reset gaps before alignment? = OFF
8. Toggle screen display = ON
9. Output format options

   1. Toggle FastaFormat output = OFF

   2. Toggle Clustal format output = ON
   3. Toogle GCG/MSF format output = OFF
   4. Toogle PHYLIP format output = OFF
   5. Toogle NEXUS format output = OFF
   6. Toogle GDE format output = OFF
   7. Toogle GDE output case = LOWSE
   8. Toogle ClustalW sequence numbers = OFF
   9. Toogle output order = ALIGNED
   10. Toogle parameter output = OFF
   11. Toogle sequence range numbers = OFF

Profile / Structure Alignments

[Profile]/Structure alignment를 수행한다. 세부메뉴는

1. Input 1st. profile
2. Input 2nd. profile/sequences
3. Align 2nd. profile to 1st. profile
4. Align sequences to 1st. profile (Slow/Accurate)
5. Toggle Slow/Fast pairwise alignments = SLOW
6. Pairwise alignment parameters
7. Multiple alignment parameters
8. Secondary structure options
   1. Use profile 1 secondary structure / penalty mask = YES
   2. Use profile 2 secondary structure / penalty mask = YES
   3. Output in alignment = secondary structure
   4. Helix gap penalty : 4
   5. Strand gap penalty : 4
   6. Loop gap penalty : 1
   7. Secondary structure terminal penalty : 2
   8. Helix terminal positions within : 3 outside : 0
   9. Strand terminal positions within : 1 outside : 1

Phylogenetic trees

PhylogeneticTree를 생성한다. 세부메뉴로

1. Input an alignment
2. Exclude positions with gaps? = OFF
3. Correct for multiple substitutions? = OFF
4. Draw tree now
5. Bootstrap tree
6. Output format options
   1. Toggle Clustal format tree output = OFF

   2. Toogle PHYLIP format tree output = ON

   3. Toggle PHYLIP distance matrix output = OFF

   4. Toggle Nexus format tree output = OFF

   5. Toogle PHYLIP boostrap positions = BRANCH LABELS / NODE LEBELS

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