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MALT index builder (version 0.5.3+galaxy0)
Use the DNA setting For RNA sequences
Used only if the reference sequences are Protein sequences

Notice: Values for Name and ID of sequence will be generated automatically if left blank.

What it does

Takes a reference sequence database (represented by a FastA file, possibly in gzip format) as input and produces an index that can be used by the malt tool as input. If MALT is to be used as a taxonomic and/or functional analysis tool as well as an alignment tool, then this MALT index builder tool must be provided with a number of mapping files that are used to map reference sequences to taxonomic or functional classes or to locate genes in DNA reference sequences.

Options

  • Specify protein alphabet reduction - specify the alphabet reduction in the case of protein reference sequences.
  • Specify seed settings - specify the settings for controlling how MALT uses its seed-and-extend approach based on “spaced seeds”.
  • Shapes - specify the seed shapes used. For DNA sequences, the default seed shape is: 111110111011110110111111. For protein sequences, by default MALT uses the following four shapes: 111101101110111, 1111000101011001111, 11101001001000100101111 and 11101001000010100010100111.
  • Maximim hits per seed - specify the maximum number of hits per seed - MALT uses this to calculate a maximum number of hits per hash value.