PanGEA-SW can be used to create pairwise sequence alignments using either the normal Smith-Waterman algorithm or the homopolymer Smith-Waterman algorithm. The pairwise alignments may be used for SNP identification with PanGEA-SNP A database sequence will be aligned with all subsequent query sequences. Minimum commands in Windows: Minimum commands in Linux (Mono): Following, for sake of simplicity, only the windows commands are shown, the Linux commands have to be adjusted as shown above:. If no output file has been specified the default output file "result.aln" is used. Multiple input files may be specified The penalties and the hit score may be specified The unmodified Smith-Waterman algorithm may be used instead of the homopolymer SW algorithm, by raising the '-normalsw' flag. Display the help
Description of all parameters:
The input file has to be a slightly modified multiple fasta file, in which two types of sequences are distinguised: database sequences and query sequences. The fasta identifier of the database sequences has to be '>>' whereas for the query sequences the common fasta identifier '>' is used. A database sequence will be aligned with all of the following query sequences until a new database sequence is encountered. download example input Example: >>data1 >query1.1 >query1.2 >>data2 >query2.1 >query2.2
Output is a PanGEA-BlastN pairwise alignment format. The output of PanGEA-SW may be used for SNP identification using PanGEA-SNP |
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