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Computational Molecular Biology 2014, Vol. 4, No. 11 1-13
http://cmb.biopublisher.ca
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several important features of five species such as GC
content, conserved genes across legumes and other
plant species, assignment of functional categories by
GO terms and identification of SSRs by MISA tool.
It is noted that this study of five different legume
species which are
Arachis hypogaea
L.,
Cicer
arietinum
L.,
Phaseolus vulgaris
L.,
Trigonella
foenum-graecum
L. and
Vicia sativa
L. will be useful
for further functional genomics studies as it includes
useful information of each species with full
annotation.
Figure 14 shows the home page of De novo RNA-Seq
data page. User has to select first platform either
Roche 454 or Illumina then select species in second
option and finally select contig. After click on Submit
button, it will give full information of that contig as
shown in Figure 15. Figure 15 the result of contigs
number 10017 of
Arachis hypogea
L.
Figure 14 Home page for De novo RNA-Seq data retrieval
The result shows various different information of the
one contigs from various databases and useful
information like, Species Name, Name of contigs,
Fasta Sequence, Sequence Length, Blast E-value Min,
Blast Similarity Mean, Blast GO number, Top-Hit
Species, Blast Hit Description (HSP), Blast Hit Gene
Name, Blast Hit Accession, Blast Hit E-value, Blast
Hit Length, Blast Hit Align Length, Blast Hit
Positives, Blast Hit Similarity, Blast Hsp/Hit, Blast
Hsp/Query, Blast Hit Query Frame, Blast Hit Uniprot,
Blast Hit Score, Blast Hit GOs, GO Accession, GO
Names, Enzyme codes, InterPro Ids, InterPro GO
Acession, InterPro GO Names, InterPro Motif Detail,
InterPro Motif Matches, Number of Blast Hits,
Enzymes, KeggMaps followed by KEGG pathway
image if any contigs is involved in any pathway.
There are total 82,505 records of contigs are
inserted, which includes 10824 contigs of
Arachis
hypogaea
L., 34678 contigs of
Cicer arietinum
L.,
6999 contigs of
Phaseolus vulgaris
L., 7256 contigs
of
Trigonella foenum-graecum
L. and 22748 contigs
of
Vicia sativa
L.
3 Glossary
It discusses various botanical terms which are useful
to identify any plant species. User has to select
Glossary option which is on left side in GLDB
database.
4 Publication
This section contains list of Publication which are
outcome of this database.