Computational tools and Interoperability in Comparative ... - CBS

Comparative Genomics
the publicly available Vibrio genomes. Output the command is listed in appendix D.2.
Listing 2.3: Using queryGenomes to obtain genome meta data.
1 # download client script
2 wget http :// www . cbs . dtu .dk/ws/ GenomeAtlas / examples / querygenomes .pl
3
4 # download XML :: Compile helper script
5 wget http :// www . cbs . dtu .dk/ws/ GenomeAtlas / examples /xml - compile .pl
6
7 # extract AT - content and number of genes for all vibrio genomes
8 perl querygenomes .pl - hideMerged - organism vibrio -output
ATCONTENT , NGENES
2.2.3 Tools contigsort and contigmap
For some applications in analysis of unfinished or partially sequenced genomes, it is desired
to obtain approximate coordinates of the contigs within the complete chromosome. To
resolve this the contigsort program was written. It accepts any number of entries (contigs)
in one FASTA file together with a backbone sequence in one contig in a second FASTA file.
The entries of the contig file is then mapped to the backbone sequence using a nucleotide
BLAST, assuming at least one significant hit. The tool then sorts all contigs based on the
coordinate in the backbone of the center-point of each alignment. Contigs spanning the
origin of circular backbones are automatically split in two.
The tool genomemap was written to visualize genome homology between two genomes
sequences. Each genome may consist of one or more contigs and all contigs are aligned
using BLASTN. This tool allow a user to validate the output of the backbone mapping from
contigsort. The plot generated has similarities to that produced by Artemis Comparison
Tool (ACT) (Rutherford et al., 2000); however the output of genomemap is a vector
graphic file (PostScript) and allows for multiple sequence entries within each of the two
compared sequences.
Example: Campylobacter jejuni str. 260.94
The 10 contigs of the currently unpublished sequence of Campylobacter jejuni str. 260.94
(GenBank accession no. AANK01000001-AANK01000010) were downloaded and converted
into FASTA format file. The program saco convert is an in-house program at CBS,
which converts between different sequence formats. In the example provided the Campylobacter
jejuni str. NCTC 11168 (Parkhill et al., 2000) is used as the backbone (see listing
2.4).
Listing 2.4: Using contigsort to map assemblied contigs to a backbone.
1 set path = (˜ pfh/scripts/contigsort ˜pfh/scripts/fetchgbk $path )
2 fetchgbk −a AANK01000001−AANK01000010 > AANK . gbk
3 saco_convert −I genbank −O fasta AANK . gbk > AANK . fsa
4 fetchgbk −a AL111168 > AL111168 . gbk
5 saco_convert −I genbank −O fasta AL111168 . gbk > AL111168 . fsa
6 contigsort −c −i AANK . fsa −b AL111168 . fsa > mapped . fsa
To visualize the result of the contig mapping the mapped and un-mapped contigs were
processed by contigmap. The output from the comparison is a PostScript document (figure
2.1 and listing 2.5).
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