blastSequences {annotate}R Documentation

Run a blast query to NCBI for either a string or an entrez gene ID and then return a series of MultipleAlignment objects.

Description

This function sends a query to NCBI as a string of sequence or an entrez gene ID and then returns a series of MultipleAlignment objects.

Usage

  blastSequences(x, database, hitListSize, filter, expect, program)

Arguments

x

A sequence as a character vector or an integer corresponding to an entrez gene ID.

database

Which NCBI database to use.

hitListSize
filter
expect

How many hits do you hope to get back, this will put a limit on the amount.

program

Which program do you want to use for blast. Default value is blastn.

Details

Right now the function only works for "blastn".

Value

a series of MultipleAlignment objects of the appropriate type.

Author(s)

M. Carlson

Examples

## x can be an entrez gene ID
blastSequences(17702)

## or x can be a sequence
blastSequences(x = "GGCCTTCATTTACCCAAAATG")

## hitListSize does not promise that you will get the number of matches you
## want..  It will just try to get that many.
blastSequences(x = "GGCCTTCATTTACCCAAAATG", hitListSize="20")

[Package annotate version 1.32.1 Index]