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Multiple alignment
Anders Gorm Pedersen (gorm@cbs.dtu.dk)
Exercise
Perform a multiple alignment of protein sequences
from HIV using the program ClustalX. The multiple alignment will later be
used in a phylogenetic analysis of different immuno-deficiency viruses.
Transparencies
Below is a list of all transparencies used for the lecture on multiple alignment. All files are in PDF format.
NOTE: PDF files are a bit large but hopefully they will print with few
problems.
Filename Size (kB) Filename Size (kB)
mulalign1.pdf 337 mulalign9.pdf 331
mulalign2.pdf 337 mulalign10.pdf 336
mulalign3.pdf 362 mulalign11.pdf 334
mulalign4.pdf 337 mulalign12.pdf 333
mulalign5.pdf 351 mulalign13.pdf 330
mulalign6.pdf 366 mulalign14.pdf 327
mulalign7.pdf 331 mulalign15.pdf 336
mulalign8.pdf 332
Some programs available on the web
- ClustalW at the European Bioinformatics Institute
- ClustalW at PBIL
- ClustalW at Institut Pasteur
- PRRN:
progressive multiple alignment with iterative refinement.
- treealign: simultaneous alignment and reconstruction of
phylogeny.
Downloadable software
- ClustalX:
popular multiple alignment tool with graphical user interface.
- PRRN:
progressive multiple alignment with iterative refinement.
- SAGA: (multiple) Sequence Alignment by Genetic Algorithm.
- DIALIGN: a
program for local multiple alignments.
Additional resources
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