seqLoGo is able to extract these information for sequence motifs shown below
- Base counts
- GC contents (-gc option)
- Amino acid or any characters counts (-any option)
- Compressed sequences (-str num option)
from quite a few of sequences.
About sequence logo in the field of biology, please refer http://weblogo.berkeley.edu.
This package is useful when you would like to make sequence logos during genome-wide analysis. Previous sequence logo software products cannot deal with too many sequences. And seqLoGo provides reduced sequences which produce the same logo in the accuracy of (-str num).
Please type
% go get github.com/carushi/seqLoGo
and you can get a seqLoGo binary file in $GOPATH/bin.
Here is an example.
% seqLoGo -input_file temp.txt -gc
% seqLoGo -input_file temp.fa -any -fasta
% seqLoGo -any -str 20 (-> Stdin)
- Write test code.
- Produce an image of sequence logo directly.