Goanna protocols

View Goanna computational protocol

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Associated diseases

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Goanna specifications

Information


Unique identifier OMICS_22590
Name Goanna
Interface Web user interface
Restrictions to use None
Input data Some protein accessions and a list of either nucleotide or protein sequences.
Input format TSV+FASTA
Output format HTML,TSV
Computer skills Basic
Stability Stable
Maintained Yes

Additional information


http://www.agbase.msstate.edu/help/annahelp.htm http://www.agbase.msstate.edu/Education/NABDAWorkshop/tutorial_4/tutorial_4.htm

Goanna in pipelines

 (8)
2017
PMCID: 5387025
PMID: 28097424
DOI: 10.1007/s00705-016-3180-5

[…] was a protein score confidence interval (c.i. %) ≥95%., spot identities were submitted to goretriever (http://www.agbase.msstate.edu/) to obtain the go annotations. if no annotation was returned, goanna was used to retrieve go annotations assigned based on sequence similarity. the resulting annotations were summarized based on the goa and whole proteome goslim set using goslimviewer []., […]

2015
PMCID: 4456163
PMID: 26042666
DOI: 10.1371/journal.pone.0128350

[…] with a perl script to query the ensembl database using the ensembl perl application program interface (api). transcripts that lacked annotation information were annotated using the genome-to-seq and goanna for go annotations based on sequence homology by basic local alignment search tool (blast) at agbase []. a two-tiered approach was taken to detect pathway level changes in gene ontology […]

2015
PMCID: 4456163
PMID: 26042666
DOI: 10.1371/journal.pone.0128350

[…] of total mapped reads estimated by tophat [] was 17 m, for an average of 65.38% paired reads mapped. all transcripts were annotated using the ensembl perl api or agbase tools [], genome2seq and goanna. a total of 16,101 genes were analyzed after filtering out lowly expressed genes. correlations among mean gene expression levels between both the h and l groups was high (r = 0.99)., the deseq […]

2015
PMCID: 4620937
PMID: 26526746
DOI: 10.4137/BBI.S30525

[…] for an input gene list and goslimviewer summarizes go annotations at a higher level. for bovine gene products that lack go, functional domains with go annotations in other species are identified by goanna by a basic local alignment search tool (blast) search, enabling the transfer of go annotations from other species to bovine gene products, when appropriate. recognizing that not all gene […]

2015
PMCID: 4620937
PMID: 26526746
DOI: 10.4137/BBI.S30525

[…] is possible to retrieve the available functional go information using the agbase tool goretriever and summarize the go using goslimviewer. for a set of bovine genes that lack functional annotation, goanna at agbase can add gos based on sequence homology. pathways resources such as reactome,, kegg, unipathways, innatedb, tfdb, and hpidb can each add additional bits of relevant information […]


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Goanna in publications

 (47)
PMCID: 5748719
PMID: 29261115
DOI: 10.3390/genes8120401

[…] carried out using two different approaches. first, we used tools available at the mississippi state university agbase portal (version 2.0) [] to assign ontologies to the transcripts of interest. goanna annotates genes by transferring ontologies based on sequence homology, and goslim further summarizes the results by providing a high-level annotation to analyzed genes. basic local alignment […]

PMCID: 5571215
PMID: 28839262
DOI: 10.1038/s41598-017-06574-5

[…] at all, at the cost of procuring only a small part of any prey item that is detected (e.g., )? should australian martu women hunt for large but difficult-to-catch kangaroo, or ubiquitous but small goanna lizards? individuals vary in their propensity to select the riskier of the possible strategies at these day-to-day decision points, as well as in their risk-related choices at crucial […]

PMCID: 5672588
PMID: 29200920
DOI: 10.3897/zookeys.689.12021

[…] knob summit, 6.xii.1998–6.ii.1999, 17°39's, 145°30'e, 1100 m, monteith & cook leg., intercept (qm); 3 specs., mcafee’s lookout, 27°26's, 152°53'e, 300 m, 18.x.1999, g.b. monteith, under dead goanna (qm); 7 specs., fraser island, yidney scrub nr. vb52, 1.–2.xii.1975, g. thompson & a. slater (qm); 1 spec., russel r., at bellenden, ker landing, 5 m, 24.x.–9.xi.1981, baited window trap […]

PMCID: 5460889
PMID: 28542225
DOI: 10.1371/journal.pntd.0005503

[…] clinics, schools and community work-places because they viewed trachoma elimination as everyone’s business []. all resources featured the program mascot—milpa (eye in warlpiri language) the trachoma goanna and the slogans "clean faces, strong eyes" and “wash your face whenever its dirty” to support new social norms for facial cleanliness. clinic materials included clinical training tools […]

PMCID: 5387025
PMID: 28097424
DOI: 10.1007/s00705-016-3180-5

[…] was a protein score confidence interval (c.i. %) ≥95%., spot identities were submitted to goretriever (http://www.agbase.msstate.edu/) to obtain the go annotations. if no annotation was returned, goanna was used to retrieve go annotations assigned based on sequence similarity. the resulting annotations were summarized based on the goa and whole proteome goslim set using goslimviewer []., […]


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