Fascin Methods

Methods

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Multiple Alignment

NCBI BLAST search was conducted using Fascin 1 sequence as query sequence. From the 112 sequences returned, 100 had FASTA formats and these 100 were run through the multiple-alignment program ClustalX. To help edit the remainding sequences a protDOM search was conducted on Fascin 1, and the results from the search were used. Sequences with excessive amino acids before or after Fascin 1 were deleted, as well as sequences with large gaps, and finally multiple results from the same organism were cleared. A final alignment was conducted on the remainding 32 sequences.

Phylogenetic Tree

Two methods were use to construct the Phylogenetic Tree.

The first used "phlip" software. Using the clustalX alignment, sequences were run through "protdist" to attain a distance matrix calcuation. The resulting data was then constructed into a tree using the neighbor-joining method, where the data was run through the phlip generation program "neighbor". Bootstrapping was conducted using the phlip programs and the original ClustalX alignment and were added the the tree created during neighbor-joining.

The second program utilised MEGA4 software, where the alignment data was formed into a bootstrap neighbor-joining method, with 500 replications.

• Sandra L. Baldauf
  

Phylogeny for the faint of heart: a tutorial
TRENDS in Genetics Vol.19 No.6 June 2003, 345-351.