Institute of Information Science and Genomics Research Center, Academia Sinica, Taiwan

GR-Aligner: a global alignment algorithm for aligning pairwise genomic sequences with rearrangement events

(submitted to Bioinformatics)

Software Download

You can download the beta version of GR-Aligner for windows here or for linux here.

Usage:

1. Please put the executable file of bl2seq in the same directory with GR-Aligner.

2. run

GR_Aligner input_file1 input_file2,

- input_file1 and input_file2 contain the input sequences in fasta format.

3. The alignment result will be in the file “output.fa”.

Simulation Data Download

Usage: In these following files, each simulated event is represented as a set of four lines,

Line1 Header information (ID, chromosome name (specise1), start position (specise1), end position (specise1), chromosome name (specise2), start position (specise2), end position (specise2), strand)

Line2 Sequence of specise1

Line3 Sequence of specise2

Line4 Positions of the introduced breakpoints

1. Inversion

o Human – Chimp (Breakpoint region identity: 0.9, 0.8, 0.7, All)

o Human – Orangutan (Breakpoint region identity: 0.9, 0.8, 0.7, 0.6, 0.5, All)

o Mouse – Rat (Breakpoint region identity: 0.9, 0.8, 0.7, 0.6, 0.5, All)

o D. melanogaster – D. simulans (Breakpoint region identity: 0.9, 0.8, 0.7, 0.6, 0.5, All)

2. Transposition

o Human – Chimp (Breakpoint region identity: 0.9, 0.8, 0.7, All)

o Human – Orangutan (Breakpoint region identity: 0.9, 0.8, 0.7, 0.6, 0.5, All)

o Mouse – Rat (Breakpoint region identity: 0.9, 0.8, 0.7, 0.6, 0.5, All)

o D. melanogaster – D.simulans (Breakpoint region identity: 0.9, 0.8, 0.7, 0.6, 0.5, All)

Aligned sequences Download

Human - Chimp

Inversion (alignment results in fasta format )

Transposition (alignment results in fasta format)

For any questions, please contact us.