blast_malavi: BLAST MalAvi
In vincenzoaellis/malaviR: An R interface to MalAvi

Description Usage Arguments Details Value Note Author(s) References Examples

View source: R/blast_malavi2.r

A function for comparing a cytochrome b DNA sequence with those in the MalAvi database.

1	blast_malavi(sequence, evalue = 1e-80, hits = 5, print.alignments = FALSE)

`sequence`	Sequence to BLAST.
`evalue`	Threshold for finding real hits. Should be a low number. Defaults to 1e-80.
`hits`	Number of hits to return. Defaults to 5.
`print.alignments`	Should the pairwise alignments be printed? Defaults to FALSE.

The function submits the sequence to the BLAST program on the MalAvi website and returns the result in a useful format.

hits are "matching" sequences.

An object of class data.frame with resulting hits and information regarding how well they match the input sequence. If no hits were found a message will print asking you to check your input sequence.

Perfect.Match in the output data frame refers to whether the pairwise alignments were identical irrespective of the coverage (e.g., an input sequence with low coverage could still generate, and often will generate, a perfect match with one or more sequences in MalAvi).

Vincenzo A. Ellis vincenzoaellis@gmail.com

Bensch S, Hellgren O, and Perez-Tris J. 2009. MalAvi: a public database of malaria parasites and related haemosporidians in avian hosts based on mitochondrial cytochrome b lineages. Molecular Ecology Resources 9: 1353-1358.

http://mbio-serv2.mbioekol.lu.se/Malavi/blast.html

## define a sequence. This is the Plasmodium parasite ACAGR1
ACAGR1 <- "GCAACTGGTGCTTCATTTGTATTTATT
TTAACTTATTTACATATTTTAAGAGGATTAAATTATTC
ATATTCATATTTACCTTTATCATGGATATCTGGATTAA
TAATATTTTTAATATCTATAGTAACAGCTTTTATGGGT
TACGTATTACCTTGGGGTCAAATGAGTTTCTGGGGTGC
TACCGTAATAACTAATTTATTATATTTTATACCTGGAC
TAGTTTCATGGATATGTGGTGGATATCTTGTAAGTGAC
CCAACCTTAAAAAGATTCTTTGTACTACATTTTACATT
TCCTTTTATAGCTTTATGTATTGTATTTATACATATAT
TCTTTCTACATTTACAAGGTAGCACAAATCCTTTAGGG
TATGATACAGCTTTAAAAATACCCTTCTATCCAAATCT
TTTAAGTCTTGATATTAAAGGATTTAATAATGTATTAG
TATTATTTTTAGCACAAAGTTTATTTGGAATACT"
blast_malavi(ACAGR1)