Help With the Role of Nomination
Help with BLAST tool
Help With Searching
Introduction
General Rules
Main Search Strategies
Help With the Rule of Nomination
LMC-000332
LMS-000183
Species name is LM, abbreviation for Locusta Migratoria. "Contig" versus "singlet" is discriminated by the one-letter code "C" or "S". Cluster numbers start at 000001 and have 6 digits. You should use this item for search only when you know the cluster name(s) for your sequence(s) of interest.
Examples:
LM_GB5_000047
LM_SH5_000436
In these examples, G represents for gregarious phase, S for solitarious phase, B for body , H for head, M for midgut and L for hind-leg , number 5 for five-instar nymph.
Unigene Name
The rule of nomination is [Species name][Contig or Singlet]-[Cluster number]LMC-000332
LMS-000183
Species name is LM, abbreviation for Locusta Migratoria. "Contig" versus "singlet" is discriminated by the one-letter code "C" or "S". Cluster numbers start at 000001 and have 6 digits. You should use this item for search only when you know the cluster name(s) for your sequence(s) of interest.
EST Name
EST name is defined as [Species name (abbr.)] _ [Library name] _ [EST number]Examples:
LM_GB5_000047
LM_SH5_000436
In these examples, G represents for gregarious phase, S for solitarious phase, B for body , H for head, M for midgut and L for hind-leg , number 5 for five-instar nymph.
Help with BLAST tool
BLAST tool
This analysis tool is based on the results from BLAST against the cluster sequences in the database, performed by using NCBI Non-Redundant protein data, NCBI Non-Redundant nucleotide data and SWISS_PROT protein data as queries. If any questions about the BLAST tool, please refer to the FAQ of BLAST.Help With Searching
Logic rules are applied in the search tool to facilitate users with their search intentions. The search logic rules related with digits include five selectable terms in the selective text box: "equals", "not equals", "not less", "not bigger", "bigger and less". The search logic rules related with word or phrase consist of four selectable terms in the selective box: "equals", "contain", "begin with", "end with".
"Equals" means that the phrase inputted matches the one in the database completely. Input the phrase "cadherin-like membrane protein [Bombyx mori]", and users will select "equals" in the selective box and retrieve the unigene LMS_000004.(Note: Annotation of the unigene LMS_000004 in this database is "cadherin-like membrane protein [Bombyx mori]")
"Contains" means that the word or phrase inputted is one part of the annotation phrase or digits, no matter which part the word or phrase is in the annotation phrase or digits.
"Begin with" means that the word or phrase inputted is at the beginning part of the annotation phrase or digits.
"End with" means that the word or phrase inputted is at the end part of the annotation phrase or digits.
If clients are not sure that the specific phrase matches the one in the subgroup of this database, we suggest clients choose "contain" for retrieval.
Queries can be combined with operators, "And" or "Or".
Enter the unigene name into the appropriate box in QuickSearch or in the specific unigene section of the Search page. This will uniquely identify the specific unigene, and it is unnecessary to input data or words in the other search box, though other available fields can be used. Users may input the unigene annotation keywords in Genbank for retrieval, and they may choose "contain", begin with" or "end with" in the selective box. If users have already known the specific phrase same to the annotation recorded in the database, they may choose "equals" for retrieval. And vice versa, they may choose "contain" in the selective box.
Example:
The BLAST_NR annotation of unigene LMS_000004 incorporating in this database is "cadherin-like membrane protein [Bombyx mori]".
Input the phrase "cadherin-like membrane protein [Bombyx mori]", and users will select "equals" in the selective box and retrieve the unigene LMS_000004.
Input the phrase"cadherin-like membrane protein" or any words in this phrase, users will choose "contain" in the selective box to retrieve the unigene including LMS_000004 that their annotation contain specific words.
Gene Ontology(GO)
In the GO search, users can input the gene ontology ID or terms to perform unigene Gene Onotology search. The GO terms in our database is stored according to the form"GO:0005509 (GO ID) " and "calcium ion binding(GO Term)", we will take the following as an example to explain the search strategy for efficient use.
Example:
GO terms incorporating in this database are "GO: 0005509"and "calcium ion binding". In order to retrieve the unigene annotated by this term, we may do the following:
GO terms incorporating in this database are "GO: 0005509"and "calcium ion binding". In order to retrieve the unigene annotated by this term, we may do the following:
InterPro
InterPro is searched for IPR accession number or terms. The InterPro annotation in our database is stored according to the form"IPR000694" or "Proline-rich region(IPR accession number or Term)", we will take the following as an example to explain the search strategy for efficient use.
And if users input any word or digits that contains in the IPR accession number or Term and choose "contain", all the unigene conforming to this rule will be retrieved.
COG (conserved orthologous genes)
The detailed information of COG may be found in the COG website
In the COG search, go to COG entry with COG name with the form "COGxxxx"where the x's are digits
Proteins in the COG database are stored by their gene names, not the full protein names. Input the protein name of COG and choose "equals" or "contain", and the retrieved unigene will be spread in the result page.
From the column "COG Class" and "Function Class", users just put the keywords and choose contain in the selective box, and the category of unigenes that perform the specific function can be found.
Blast result search
Results of BLAST searches using the specified assembly as a query against the NCBI Non-Redundant protein sequences are summarized. Results with low e-value (e-value< 1e-5) are shown. Links to the GenBank pages and raw BLAST results are provided. The search strategy is the same to Unigene annotation search.
Introduction
When searching for the detailed information of the unigene, precise search will run faster and be more likely to return the actual unigenes of interest. For best results, enter the minimum amount of information needed to uniquely identify the unigenes, such as Unigene_Name, GO ID, and COG_Name.General Rules
There are two main search tools: QuickSearch and the Advanced Search page. Use QuickSearch for simple queries. QuickSearch is found on the most interior portal pages. Users can enter into the search page by clicking the "search" icon on the navigation bar. The search page allows users to control additional features from several analysis aspects: Unigene basic information, GO, COG, InterPro, KEGG, BLAST_NR, BLAST_NT and BLAST_SWI analysis results.Logic rules are applied in the search tool to facilitate users with their search intentions. The search logic rules related with digits include five selectable terms in the selective text box: "equals", "not equals", "not less", "not bigger", "bigger and less". The search logic rules related with word or phrase consist of four selectable terms in the selective box: "equals", "contain", "begin with", "end with".
"Equals" means that the phrase inputted matches the one in the database completely. Input the phrase "cadherin-like membrane protein [Bombyx mori]", and users will select "equals" in the selective box and retrieve the unigene LMS_000004.(Note: Annotation of the unigene LMS_000004 in this database is "cadherin-like membrane protein [Bombyx mori]")
"Contains" means that the word or phrase inputted is one part of the annotation phrase or digits, no matter which part the word or phrase is in the annotation phrase or digits.
"Begin with" means that the word or phrase inputted is at the beginning part of the annotation phrase or digits.
"End with" means that the word or phrase inputted is at the end part of the annotation phrase or digits.
If clients are not sure that the specific phrase matches the one in the subgroup of this database, we suggest clients choose "contain" for retrieval.
Queries can be combined with operators, "And" or "Or".
Main Search Strategies
UnigeneEnter the unigene name into the appropriate box in QuickSearch or in the specific unigene section of the Search page. This will uniquely identify the specific unigene, and it is unnecessary to input data or words in the other search box, though other available fields can be used. Users may input the unigene annotation keywords in Genbank for retrieval, and they may choose "contain", begin with" or "end with" in the selective box. If users have already known the specific phrase same to the annotation recorded in the database, they may choose "equals" for retrieval. And vice versa, they may choose "contain" in the selective box.
Example:
The BLAST_NR annotation of unigene LMS_000004 incorporating in this database is "cadherin-like membrane protein [Bombyx mori]".
Input the phrase "cadherin-like membrane protein [Bombyx mori]", and users will select "equals" in the selective box and retrieve the unigene LMS_000004.
Input the phrase"cadherin-like membrane protein" or any words in this phrase, users will choose "contain" in the selective box to retrieve the unigene including LMS_000004 that their annotation contain specific words.
Gene Ontology(GO)
In the GO search, users can input the gene ontology ID or terms to perform unigene Gene Onotology search. The GO terms in our database is stored according to the form"GO:0005509 (GO ID) " and "calcium ion binding(GO Term)", we will take the following as an example to explain the search strategy for efficient use.
Example:
GO terms incorporating in this database are "GO: 0005509"and "calcium ion binding". In order to retrieve the unigene annotated by this term, we may do the following:
GO terms incorporating in this database are "GO: 0005509"and "calcium ion binding". In order to retrieve the unigene annotated by this term, we may do the following:
InterPro
InterPro is searched for IPR accession number or terms. The InterPro annotation in our database is stored according to the form"IPR000694" or "Proline-rich region(IPR accession number or Term)", we will take the following as an example to explain the search strategy for efficient use.
And if users input any word or digits that contains in the IPR accession number or Term and choose "contain", all the unigene conforming to this rule will be retrieved.
COG (conserved orthologous genes)
The detailed information of COG may be found in the COG website
In the COG search, go to COG entry with COG name with the form "COGxxxx"where the x's are digits
Proteins in the COG database are stored by their gene names, not the full protein names. Input the protein name of COG and choose "equals" or "contain", and the retrieved unigene will be spread in the result page.
From the column "COG Class" and "Function Class", users just put the keywords and choose contain in the selective box, and the category of unigenes that perform the specific function can be found.
Blast result search
Results of BLAST searches using the specified assembly as a query against the NCBI Non-Redundant protein sequences are summarized. Results with low e-value (e-value< 1e-5) are shown. Links to the GenBank pages and raw BLAST results are provided. The search strategy is the same to Unigene annotation search.