gl.blast: Aligns nucleotides sequences against those present in a...

In green-striped-gecko/dartR: Importing and Analysing 'SNP' and 'Silicodart' Data Generated by Genome-Wide Restriction Fragment Analysis

Aligns nucleotides sequences against those present in a target database using blastn

Description

Basic Local Alignment Search Tool (BLAST; Altschul et al., 1990 & 1997) is a sequence comparison algorithm optimized for speed used to search sequence databases for optimal local alignments to a query. This function creates fasta files, creates databases to run BLAST, runs blastn and filters these results to obtain the best hit per sequence.

This function can be used to run BLAST alignment of short-read (DArTseq data) and long-read sequences (Illumina, PacBio... etc). You can use reference genomes from NCBI, genomes from your private collection, contigs, scaffolds or any other genetic sequence that you would like to use as reference.

Usage

gl.blast(
  x,
  ref_genome,
  task = "megablast",
  Percentage_identity = 70,
  Percentage_overlap = 0.8,
  bitscore = 50,
  number_of_threads = 2,
  verbose = NULL
)

Arguments

x	Either a genlight object containing a column named 'TrimmedSequence' containing the sequence of the SNPs (the sequence tag) trimmed of adapters as provided by DArT; or a path to a fasta file with the query sequences [required].
ref_genome	Path to a reference genome in fasta of fna format [required].
task	Four different tasks are supported: 1) “megablast”, for very similar sequences (e.g, sequencing errors), 2) “dc-megablast”, typically used for inter-species comparisons, 3) “blastn”, the traditional program used for inter-species comparisons, 4) “blastn-short”, optimized for sequences less than 30 nucleotides [default 'megablast'].
Percentage_identity	Not a very sensitive or reliable measure of sequence similarity, however it is a reasonable proxy for evolutionary distance. The evolutionary distance associated with a 10 percent change in Percentage_identity is much greater at longer distances. Thus, a change from 80 – 70 percent identity might reflect divergence 200 million years earlier in time, but the change from 30 percent to 20 percent might correspond to a billion year divergence time change [default 70].
Percentage_overlap	Calculated as alignment length divided by the query length or subject length (whichever is shortest of the two lengths, i.e. length / min(qlen,slen) ) [default 0.8].
bitscore	A rule-of-thumb for inferring homology, a bit score of 50 is almost always significant [default 50].
number_of_threads	Number of threads (CPUs) to use in blastn search [default 2].
verbose	verbose= 0, silent or fatal errors; 1, begin and end; 2, progress log ; 3, progress and results summary; 5, full report [default 2 or as specified using gl.set.verbosity]

Details

Installing BLAST

You can download the BLAST installs from: https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/

It is important to install BLAST in a path that does not contain spaces for this function to work.

Running BLAST

Four different tasks are supported:

• “megablast”, for very similar sequences (e.g, sequencing errors)

• “dc-megablast”, typically used for inter-species comparisons

• “blastn”, the traditional program used for inter-species comparisons

• “blastn-short”, optimized for sequences less than 30 nucleotides

If you are running a BLAST alignment of similar sequences, for example Turtle Genome Vs Turtle Sequences, the recommended parameters are: task = “megablast”, Percentage_identity = 70, Percentage_overlap = 0.8 and bitscore = 50.

If you are running a BLAST alignment of highly dissimilar sequences because you are probably looking for sex linked hits in a distantly related species, and you are aligning for example sequences of Chicken Genome Vs Bassiana, the recommended parameters are: task = “dc-megablast”, Percentage_identity = 50, Percentage_overlap = 0.01 and bitscore = 30.

Be aware that running BLAST might take a long time (i.e. days) depending of the size of your query, the size of your database and the number of threads selected for your computer.

BLAST output

The BLAST output is formatted as a table using output format 6, with columns defined in the following order:

• qseqid - Query Seq-id

• sacc - Subject accession

• stitle - Subject Title

• qseq - Aligned part of query sequence

• sseq - Aligned part of subject sequence

• nident - Number of identical matches

• mismatch - Number of mismatches

• pident - Percentage of identical matches

• length - Alignment length

• evalue - Expect value

• bitscore - Bit score

• qstart - Start of alignment in query

• qend - End of alignment in query

• sstart - Start of alignment in subject

• send - End of alignment in subject

• gapopen - Number of gap openings

• gaps - Total number of gaps

• qlen - Query sequence length

• slen - Subject sequence length

• PercentageOverlap - length / min(qlen,slen)

Databases containing unfiltered aligned sequences, filtered aligned sequences and one hit per sequence are saved to the temporal directory (tempdir) and can be accessed with the function gl.print.reports and listed with the function gl.list.reports. Note that they can be accessed only in the current R session because tempdir is cleared each time that the R session is closed.

BLAST filtering

BLAST output is filtered by ordering the hits of each sequence first by the highest percentage identity, then the highest percentage overlap and then the highest bitscore. Only one hit per sequence is kept based on these selection criteria.

Value

If the input is a genlight object: returns a genlight object with one hit per sequence merged to the slot $other$loc.metrics. If the input is a fasta file: returns a dataframe with one hit per sequence.

Author(s)

Berenice Talamantes Becerra & Luis Mijangos (Post to https://groups.google.com/d/forum/dartr)

References

• Altschul, S. F., Gish, W., Miller, W., Myers, E. W., & Lipman, D. J. (1990). Basic local alignment search tool. Journal of molecular biology, 215(3), 403-410.

• Altschul, S. F., Madden, T. L., Schäffer, A. A., Zhang, J., Zhang, Z., Miller, W., & Lipman, D. J. (1997). Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic acids research, 25(17), 3389-3402.

• Pearson, W. R. (2013). An introduction to sequence similarity (“homology”) searching. Current protocols in bioinformatics, 42(1), 3-1.

See Also

gl.print.history

Examples

## Not run: 
res <- gl.blast(x= testset.gl,ref_genome = 'sequence.fasta')
# display of reports saved in the temporal directory
gl.list.reports()
# open the reports saved in the temporal directory
blast_databases <- gl.print.reports(1)

## End(Not run)

green-striped-gecko/dartR documentation built on Sept. 7, 2024, 4:15 a.m.