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,
          timeout=40, as=c("DNAMultipleAlignment", "data.frame", "XML"))

### Arguments

`x` | A sequence as a character vector or an integer corresponding to an entrez gene ID. Submit multiple sequences as a length-1 character vector, `x = ">ID-1\nACATGCTA\n>ID-2\nAAACCACTT"`.
`database` | Which NCBI database to use. If not “blastn”, then set `as="XML"`
`hitListSize` | Number of hits to keep.
`filter` | Sequence filter; “L” for Low Complexity, “R” for Human Repeats, “m” for Mask lookup
`expect` | The BLAST ‘expect’ value above which matches will be returned.
`program` | Which program do you want to use for blast.
`timeout` | Approximate maximum length of time, in seconds, to wait for a result.
`as` | character(1) indicating whether the result from the NCBI server should be parsed to a list of `DNAMultipleAlignment` instances, represented as a `data.frame`, or returned as XML.

### Details

Right now the function only works for "blastn".

The NCBI URL api used by this function is documented at https://www.ncbi.nlm.nih.gov/blast/Doc/urlapi.html

### Value

By default, a series of `DNAMultipleAlignment` (see `MultipleAlignment-class` objects. Alternatively, a `data.frame` or XML document returned from the NCBI server. The `data.frame` is a ‘long form’ representation of the ‘Iteration’, ‘Hit’ and ‘Hsp’ results returned from the server. The XML document is the result of the `xmlParse` function of the XML library, and follows the format described by https://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.dtd and https://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.mod.dtd.

### Author(s)

M. Carlson

### Examples

    ## x can be an entrez gene ID
    blastSequences(17702, timeout=40, as="data.frame")

    if (interactive()) {

        ## 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 1.62.0 Index]