% tar -xvzf Cgaln-1.*.*.tar.gzThen, go to the new directory and type:
% makeCgaln requires gcc for compilation. (http://gcc.gnu.org/)
% ./maketable [options] sequenceFour kinds of file, *.seedtable, *.blktable, *.poistable and *.txt, are made in the directory ./(output directory)/ (default: CgalnTable). The seedtable and blktable for reverse complement are also constructed at the same time. If the input file is in multi-fasta format, corresponding table of all fastas is merged into one table. It should be noted that different tables are required when the user wants to use Cgaln with different block size or k-mer sizes. The options for setting specific k-mer or block size are as follows.
options: -o specify output directory (default: CgalnTable) -K# specifies k-mer size (11 as default) -BS# specifies block size (10000 as default)For example, the command
% ./maketable -K12 -BS20000 seq1.fastamakes tables for seq1.fasta with 12-mer spaced seeds and block size of 20000.
Important note: The prefix of all tables generated is the input file name. If the user makes the tables of a file which has same filename of others (e.x. ./human/chrX.fa and ./mouse/chrX.fa), the tables are overwritten. Please use different filenames for the files to compare.
% ./Cgaln [options] sequence1 sequence2 -o outputfileThe results are output to stdout with a format compatible with gnuplot, while another simple output format may be chosen with -Ens option.
options: (default in parentheses) -t: table directory (default: CgalnTable) -r: both strands (forward strand only) -b: output block level alignments (output nucleotide level alignments) -nc: no chaining (with chaining) -ia: do iterative alignment (off) -pr: print outlines of regions for iterative alignment (off) -fc: remove inconsistent colonies at the block level (off) -cs: remove inconsistent HSPs at the HSP-chaining (off) -noext: (when -ia is on) skip gapped extension of HSPs (don't skip) -sr: examine short reverse complement (off) -k#: seed weight/width; -k1: 11/18; -k2: 12/19; -k3: 13/20 (11/18) -BS#: block size (10000) -X#: X drop-off value at block-level (4000) -R#: ratio between X drop-off score and gap penalty at block-level (1500) -nl: don't insert delimiters between outputs for multifasta file (on) -otype: output format; 0: gnuplot; 1: ensfile; 2: fasta (gnuplot format)
Important note: When "-otype2 (fasta format)" is selected, the size of output file may be quite large (about several times larger than input files). This option is not appropriate for whole-genome comparisons of large genomes such as mammals.Examples:
For standard use, we recommend the option
% ./Cgaln -r -ia seq1.fasta seq2.fasta > result.dotwhich outputs the alignment result between seq1.fasta and seq2.fasta to result.dot in a format compatible with gnuplot, considering both strands and applying iterative step. If the input sequences are large (e.g. over 100 Mb), a larger k-mer is appropriate.
% ./Cgaln -r -ia -k2 seq1.fasta seq2.fasta -o result.dotwhich uses the 12-mer spaced seed. If you simply wants to take a global view of homology between two genomes, e.g. to infer evolutionary events of genome rearrangement, it is enough to output the block-level results obtained in the first stage.
% ./Cgaln -r -b seq1.fasta seq2.fasta -o result.dotwhich requires very short computational time. If the result of block level alignment looks too noisy, the value for X might be increased.
% ./Cgaln -r -ia -X6000 seq1.fasta seq2.fasta -o result.dotConversely, if the result of block level alignment looks too sparse, the value for X should be decreased.
Repetitious outputs at the block-level caused by unmasked repetitive regions can also be filtered out by -fc option. Cgaln with -fc option enforces the resultant alignments to be consistent with one another (projections of dot plots to neither axis overlap each other) at the block level.
% ./Cgaln -r -nc seq1.fasta seq2.fasta -o result.dotThe above command outputs the alignment results considering reverse strand as well and does not chain HSPs.
% ./Cgaln -R1000 seq1.fasta seq2.fasta -o result.dotThe value for R indicates the gap penalty at the block-level alignment. The smaller the score is, the larger the gap penalty is.
% ./Cgaln -r -ia -noext -sr seq1.fasta seq2.fasta -o result.dotWith -sr option, Cgaln tries to find short inversions at the NA level. In this mode, Cgaln does not perform gapped HSP extension, and examines both the forward and reverse strands within inter-HSP regions.
Nakato, R., and Gotoh, O. (2008). A novel method for reducing computational complexity of whole genome sequence alignment. In Proceedings of the 6th Asia-Pacific Bioinformatics Conference (APBC2008), pages 101-110.
Nakato, R., and Gotoh, O. (2010). " Cgaln: fast and space-efficient whole-genome alignment" BMC Bioinformatics, 11:24.