HOMD User Documentation     
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User Documentation
+Taxon Description
+Identify 16S rRNA Sequence
+Tools & Download
 >Genomics Tools Overview
 >HOMD Genome Viewer
 >HOMD JBrowse Genome Viewer
 >Dynamic Genome Annotation
 +Blast against Genomes
 >HOMD Dynamic Genomic BLAST
 >KEGG Pathway
 >Gene Ontology
 >Sequence Batch Download
+Database Search
General Documentation
+HOMD Information
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HOMD Genome Viewer
HOMD Genome Viewer provides a graphical, six-frame transnational view of the same region of the genome with individual panels showing different sets of annotations. The ability to show different sets of annotations done by different institutes is the most important and useful feature of the Genome Viewer. O­nce a genome is sequenced, it is often annotated by several institutes. For example, at least two independently annotated databases are currently available for the genomes of Porphyromonas gingivalis, Streptococcus mutans and Treponema denticola, i.e. in The Comprehensive Microbial Resource of The Institute of Genomic Research (TIGR CMR) and the Oral Pathogen Sequence Databases of Los Alamos National Laboratory (LANL), respectively. While many of these independent annotations provide unique and useful information regarding the same genomes, difficulties are often encountered when users try to compare or combine information available for the same genes. The major reason being the discrepancies among the different annotations with the regard to gene IDs or names. To alleviate this difficulty and aid the reconciliation between different annotations, the HOMD Genome Viewer provide different annotations of the same region of the genome in the same viewing panel. Below is a screen shot of Genome Viewer with detail description referenced by numbers.
1) Genome name and total length of genome (in bases) are shown here.
2) Window range The vertical length (height) of the genome viewing panel can be adjusted to 3 different sizes; this feature is sometime useful when viewing many panels at the same time to save some scrolling.
3) Range show: the total length of the genome shown in the viewing panel, and the range starting from which base to which base is clearly indicated.
4) Focus bar The viewing range (in red) and its location relative to the whole genome/contig, is proportionally drawn in this bar (in black) which represent the whole length of the genome or contig that you are viewing.
5) Genome coodination ruler provides the coordinations for the vertical lines that are shown in all viewing panels below.

6) Dynamic Annotation Panel Six-frame illustration of the BLASTP search result for all the ORFs in viewing range. The search was done by the HOMD automatic annotation pipeline and is against the weekly updated NCBI nr sequence database. The  date of the most recent update is printed to the right side of the panel. The significant of the best hits is colored according to the BLAST score. The higher the score, the darker the red color will be. The lightest gray indicates no hits were found for the corresponding ORFs. Clicking o­n the ORFs in the panel will bring up a sub menu linking to the detail information for the ORFs, including the nucleotide sequence, amino-acid sequence, original BLAST result, personal annotation and bookmark etc.
7) Additional annotation panels If other annotations are available for a particular genome, and the information is publicly available, we will download the compile the information and present it in the individual panels. Examples in the screen shot above shows additional annotations from TIGR, NCBI and Los Alamos Oralgen. Clicking o­n the ORF features will lead to (in a separate browser window) the original source (e.g., TIGR, NCBI sites) for the corresponding ORF.
8) Other genomic information panels Such as G+C content of the viewing range; example shown above also includes the microarray gene expression data.
9) Feature in focus Usually when you mouse over an ORF in any of the annotation panels above, the gene ID and the definition/best hit/gene name will be shown in a small pop-up box right next to the ORF; the same information will also be shown in this box at the same time; this is useful when you need to copy and text in this field. Sometime if the viewing range is large and too many ORFs shown in the same panel it will be difficult to mouse-over an ORF and then go to the focus field without touching other ORFs. If this is the case, try to narrow the viewing range (zoom in) so there are not too many ORFs shown in the panel.
10) Viewer Controller This panel provide functions for navigating around the genome/contig. These include: walk forward, reverse, zoom in and out, go to previous or next contig (or molecules such as a different chromosome or plasmid). You can also go down to the sequence level in which the viewing range is preset to 100-bp and the actually DNA sequence will be shown in the middle of the panel. If the genome or contig is not too big you can also quickly go to the whole-genome or whole-contig view by clicking the "whole contig view" button. You can also specify the exact range of the genome/contig that you wish to view by typing the coordinations (in bp) in the "from" and "to" field. Or if you know the ORF ID you can also specify it in the "Jump to the ORF ID" field. Available ID formats (made by different annotations) will be automatically shown in the drop down menu. Other useful navigation features include extracting the DNA sequence in the viewing range (the "get contig na or na in range" button) and to analyze the sequence in range by the wEMBOSS software package (the "Get Seq to wEMBOSS" button).
11) Select Viewer Blocks To show o­nly certain annotation of information panels, check or un-check these options will toggle the visibility of the corresponding panels.
12) GC Block Options If G+C panel is visible, these options allow you to change the range over which the average GCs were calculated.
13) Microarray OptionsTo choose different sets of microarray gene expression data, if available for the genome.
14) Genome Info This is the overall statistical summary for the entire genome, either complete of partially sequenced.
Information include number of contigs (molecules), total (combined) length (in bps), average GC, the sequence release date (when the original sequence data was release).

Article last modified on 2014-04-08 09:45:11 by lyang; viewed 1062 times; Category: User Documentation; Topic: Tools & Downloa

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