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Genomes and genes
Sequence tools ![](images/onebit_49.png)
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retrieve sequence
retrieve EnsEMBL seq fetch-sequences from UCSC
sequences from bed/gff/vcf
purge sequence
convert sequences
random sequences
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Matrix tools ![](images/onebit_49.png)
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Build control sets
Motif discovery
strings
oligo-analysis (words)
oligo-diff (words)
dyad-analysis (spaced pairs)
pattern assembly
strings with positional biais
position-analysis (words)
local-word-analysis (word and spaced pairs)
matrices
info-gibbs
Pattern matching ![](images/onebit_49.png)
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Comparative genomics ![](images/onebit_49.png)
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get orthologs
get orthologs-compara
footprint-discovery footprint-scan
NGS - ChIP-seq
Genetic variations (Var-tools) ![](images/onebit_49.png)
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Variation information
Retrieve variation sequences
Scan variations with motifs
Convert variation formats
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Conversion/Utilities
Set comparisons / enrichment
Stats
Frequency distribution
sequences
convert sequences
matrices
convert matrix / logo
background models
create background
convert background
sequence probability
features
convert features
compare features
Drawing
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