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Rationale and Background
LASTAL (or local alignment search tool aligner) is designed to perform large sequence alignments such as whole genome alignments (WGAs). This particular installation is designed specifically for WGAs, with options specifically enabled to produce high quality alignments.
Query: Path to the query file name. Nucleotide sequences in fasta format
Database: Path to the Database folder prepared by LASTDB
E-value:Expect value (E) threshold for saving hits (Default is 0.05) - note that this may be slightly different than BLAST e-values. Per the LAST e-values manual page, E is the expected number of alignments with greater or equal score, between: a random sequence with the same length as the query sequence, and a random sequence with the same length as the database. An E of 0.05 is fairly standard for WGAs.
Multiplicity: Maximum multiplicity for initial matches. Each initial match is lengthened until it occurs at most this many times in the reference. A larger number is slower but more sensitive. Default is 20, recommended maximum is 100. For more details about LAST parameters, please visit the LAST documentation page here.
Generated output files
LASTAL will generate two .maf files (multiple alignment format). The first (query_name.out.maf) will be the search results that correspond to the unique best fit from the subject genome that corresponds to each part of the query. In essence, each query base pair will be aligned to at most one subject base pair (keeping only the best alignments). This is performed within the app using LAST's last-split algorithm. The second output file (query_name.out2.maf) is generated by swapping the sequences and getting a 1-to-1 alignment by ensuring that only one copy of each query base pair is kept. This is performed using LAST's maf-swap followed by a second round of last-split. These two files can be kept to generate contiguous WGAs.
All files are located in the Community Data directory of the CyVerse Discovery Environment at the following path:
Community Data > iplantcollaborative > example_data > LAST > LASTAL (/iplant/home/shared/iplantcollaborative/example_data/LAST/LASTAL)