June 2, 2018
graphic interfaces - BioLegato borrows the concept of
objects from object-oriented databases and
object-oriented programming languages.
- launcher for BIRCH GUI programs
bldna - DNA/RNA sequences
blprotein - amino acid sequences
blnalign - work with DNA/RNA sequence alignments
blpalign - work with protein sequence alignments
bltable - spreadsheet data (early prototype)
blreads - perform tasks on sequencing reads
blmarker - molecular marker data
blncbi - search NCBI databases
blnfetch - retrieve DNA or RNA sequences from NCBI
blpfetch - retrieve amino acid sequences from NCBI
bltree - display and manipulate phylogenetic trees
birchadmin - manage a BIRCH site
blgeneric - empty BioLegato instance
|bldna is a BioLetgato instance
specialized for working with dna sequence data. The
sequence canvas is designed as a multiple sequence
alignment editor allowing the insertion and deletion of
gaps. As an alternative to using the entire alignment,
specific sections of the alignment can be selected in
blocks and used for further analysis.
|blprotein is a BioLetgato instance specialized for working with protein sequence data. It has the the same kind of sequence canvas as bldna. blprotein also uses the same methods as bldna for file input.|
|blnalign is a BioLetgato instance that performs tasks on a set of aligned DNA or RNA sequences. Tasks include various ways of displaying alignments, and construction of phylogenetic trees.|
|blpalign is a BioLetgato instance that performs tasks on a set of aligned amino acid sequences. Tasks include various ways of displaying alignments, and construction of phylogenetic trees.|
|blreads manages the many tasks on NGS
sequencing data, including:
blmarker is a BioLetgato interface specialized for molecular marker data, such as microsatellites, AFLPs, SRAPS, or many other types of molecular markers.
blnfetch is a BioLetgato interface specialized for retrieval of DNA or RNA sequences, using NCBI GI numbers or ACCESSION numbers as input.
At right, we see a blnfetch window generated from a blastn search by bldna.
The NCBI database includes an increasing number of chromosome-sized entries. SeqFetch allows the user to select the minimum and maximum length of sequences retrieved, making it easy to eliminate very large sequences.
blpfetch is a BioLetgato interface specialized for retrieval of amino acid sequences, using NCBI GI numbers or ACCESSION numbers as input.
At right, we see a blpfetch window generated from a blastp search by blprotein.