read.blast6out: Read file in blast6out format generated by USEARCH or VSEARCH

In HajkD/LTRpred: De novo functional annotation of retrotransposons

Read file in blast6out format generated by USEARCH or VSEARCH

Description

Read a file in blast6out format generated by either USEARCH or VSEARCH.

Usage

read.blast6out(blast6out.file)

Arguments

blast6out.file

to blast6out file (*.blast6out extension).

Value

A dataframe storing the following columns:

• query: query id.

• subject: subject id.

• perc_ident: pecent identity between query and subject.

• align_len: alignment length between query and subject.

• n_mismatch: number of mismathces between query and subject.

• n_gap_open: number of gap openings between query and subject.

• start_q: start position in query. Query coordinates start with 1 at the first base in the sequence as it appears in the input file. For translated searches (nucleotide queries, protein targets), query start < end for +ve frame and start > end for -ve frame.

• end_q: end position in query.

• start_s: start position in subject. Subject coordinates start with 1 at the first base in the sequence as it appears in the database. For untranslated nucleotide searches, subject start < end for plus strand, start > end for a reverse-complement alignment.

• end_s: end position in subject.

• evalue: evalue calculated using Karlin-Altschul statistics.

• bit_score: bit score calculated using Karlin-Altschul statistics.

Author(s)

Hajk-Georg Drost

Examples

# read example *.blast6out file
test.blast6out <- read.blast6out(system.file("test.blast6out", package = "LTRpred"))

# look at the format in R
head(test.blast6out)

HajkD/LTRpred documentation built on April 22, 2022, 4:35 p.m.