Contents:

Search by Fly Genes:

This documentation contains information on how to search for gene and amplicon information by fly gene symbol, CG identifier, or FBGN.

Search by DRSC Amplicon IDs:

This documentation contains information on how to search for gene and amplicon information by DRSC Amplicon ID.

Search by Genes from Non-Fly Organisms:

This documentation contains information about how search can be performed by gene name or NCBI accession from an organism aside from Drosophila melanogaster.

Search by Sequence:

This documentation contains information about how search can be performed with a sequence provided by the user.

Documentation of Search Results:

This page contains information regarding the Amplicon Details Display. The Amplicon Details Display is shown upon a successful gene or amplicon search.

Documentation of Search by Fly Genes

• Use this tool to search for information by Gene Symbol/Name, CG identifier, or FBGN (Flybase Gene ID). This tool can also be used to search by DRSC Amplicon IDs.
• This tool only allows searching by genes from Drosophila melanogaster. If a search by genes from other organisms is desired, click on the link below the text field at the top of the page. This will bring the user to the Sequence and Non-Fly Gene Search Tool.
• If the program cannot find a particular Gene Symbol, CG, FBGN, or Amplicon ID in the database, it will return the message "Cannot find 'name' in database".
• If the program finds the Gene Symbol, CG, or FBGN in the database, but cannot find any amplicons that target that gene, it will display "No amplicons found". This means the DRSC has not amplicons that have been designed to target this gene.
• If the search is successful, detailed information of the corresponding amplicon(s) is displayed. This display will include a summary of the screens which have "hits" on this particular amplicon. Additionally, sequence and gene information for the amplicon(s) is displayed. For more information of this display see the Documentation of Search Results.

Documentation of Search by DRSC Amplicon IDs

• Search can be performed by DRSC Amplicon Id using the same tool as search by gene symbol, CG, or FBGN. Its documentation is here.

Documentation of Search by Non-Fly Genes

• This tool allows the user to search the DRSC database using any sequence the user desires or to search by a non-fly gene.
• The user may provide a sequence to use for the search or the user may provide a gene name and organism name for the search. The user may not provide both a sequence and a gene name at the same time.
• If the user decides to use the gene name option, the user may enter a gene name.
• The organism name should be the scientific name of the organism.
• If a particular gene name is tried, and the program cannot find the gene in GenBank, the user should try an alternative name. The number of gene synonyms stored locally is not very high. Also, Homologene is somewhat stringent. If a less stringent search is needed, cut and paste a sequence for a Blast-based search.
• This tool uses NCBI's BLAST to search the DRSC database.
• The user must specify whether the sequence provided is nucleotide or protein.
• The user must specify an appropriate blast algorithm. Currently, the options are "blastn", "tblastn", and "tblastx". blastn and tblastx are appropriate for nucleotide query sequences. tblastn is appropriate for protein query sequences. tblastx is less stringent than blastn. More information about BLAST can be found here.
• The user must specify what target to search. Currently, there are two options: "DRSC Amplicon Set" and "BDGP 3.1 Fly Transcripts". Essentially, the former includes just the sequences of the amplicons and the latter includes entire genes. Choose the latter if a broader search is desired.
• The score threshold indicates the BLAST score that should be used as a cutoff. The more negative the score, the more stringent.
• To maximize the number of results, the user should use tblastx with a nucleotide sequence, use BDGP 3.1 as the target, and set the threshold to -5.

Documentation of Search by Sequence

• To search with a user-provided sequence use the same tool as Search by Non-Fly Genes.