Bio.Net Demo User Manual
Bio.Net demo runs under Windows 2000/XP. Recommended hardware: 512 MB
RAM or larger, high speed Internet connection.
(1) Downloading new data. Click "Demo 1" tab on the top of the
software window, as show below. Click a "Go..." button to download data from a
remote database. After downloading, the software will automatically re-format
the data in to XML format and store them at the the local computer. (The
upstream sequences and homologous gene information are not stored in XML. This
will be changed in later versions.) The paths of newly generated files
will be shown in the text bar below the "Go..." button.
(2) Building local database and detecting
inconsistencies among databases. The newly download data have not yet been
integrated with other data from other databases. To integrate them, click The
"Demo 2" tab. Choose the appropriate "Go..." button to re-integrate one of the
three local databases: human gene database, mouse gene database and rat gene
database. If inconsistent information from different databases is found while
integrating databases, such information will be saved into a .log file. A
warning message will show up and indicate where the .log file is stored. Users
can browse these .log file with a text editor.
(3) Batch information retrieval.
To retrieve all information from the integrated databases, click The "Demo 3"
tab. Click the "Load Gene List (LocusLink IDs)" button, and indicate a
file containing LocusLink IDs. The LocusLink IDs will show at the left pane of
the software window. Click on a LocusLink ID, all related information to this
gene will show up in right pane. In the right pane, click the tabs: General
information, Sequence information, Protein information, Gene Ontology, and
PubMed to view related information. Click the "Save Gene Annotation Information"
button to save the retrieved information to a file.
Choose a LocusLink ID, and click on the PubMed tab to view
all PubMed papers that are linked to this gene. Click on the PubMed ID to view
more information.
Choose a LocusLink ID, and click on the "HomoloGene" tab.
All the homologous genes, in totally 16 possible species, will be listed,
together with evidence and sequence identity information.
(4) Retrieving upstream sequences. Click "Demo
4"
tab. UCSC Genome Bioinformatics has compiled a collection of sequences 5000
bases upstream of annotated transcription start of RefSeq genes for human, mouse
and rat. The upstream sequence retrieval tool queries this upstream sequence
collection. Providing a list of RefSeq IDs, users can
choose to retrieve any lengths, up to 5000, of upstream sequences. Please
provide the path for an input file in the text bar at the top. The input file
should contain a column of RefSeq ids, like this:
NM_000014
NM_000015
NM_000016
NM_000017
NM_000018
Please indicate the appropriate species. Please indicate the length of upstream
sequences to retrieve. Put the path of the output file in the text bar at the
bottom. Click the "Retrieve!" button at the top to start retrieving. A message
box will pop up after the retrieval.
(5) Retrieving homologous genes.
Click "Demo 5" tab. In the input file, please provide
a list of LocusLink IDs of human, mouse or rat genes. At the middle of this
page, check or uncheck the target species in which the user want to retrieve
homologous genes. Click the "Retrieve!"
button at the top. The demo application will find their homologous genes in altogether 15 species*,
if applicable, from the HomoloGene database. The following information will be
stored at the user indicated output file: LocusLink id from the original user
input file, the LocusLink ID of the first homologous gene, the species of the
first homologous gene, the percent similarity between the original gene and the
first homologous gene, the type of the similarity# between the two
genes, information about the 2nd, 3rd, ..., homologous genes.
* All the species included in the HomoloGene database:
Arabidopsis thaliana, Bos taurus, Caenorhabditis elegans, Danio rerio,
Drosophila melanogaster, Homo sapiens, Hordeum vulgare, Lycopersicon esculentum,
Medicago truncatula, Mus musculus, Oryza sativa, Rattus norvegicus, Sus scrofa,
Triticum aestivum, Xenopus laevis, Zea mays.
# The types of similarity are: reciprocal
best among 3 or more organisms, reciprocal best match between 2 organisms,
curated homology relationship.
After pressing the "Retrieve!" button, information about
the user requested homologous genes will be output into the user indicated
output file. Furthermore, a XML file containing the same information will be
generated. The names and directories of the output files will be reported by a
dialog box, such as:
This site was last updated
02/22/04