Manual for the SCPD Database

Saurabh Sinha
March 7, 2000

Link to the database

Introduction

• sequences of genes and ORFs (that contain instances of known regulatory elements) by name
• detailed description and occurrences of regulatory elements and transcription factors
• tools to analyze motifs in genes and ORFs
• provision to submit information to the database
• other miscellaneous information such as binding affinities of certain motifs and links to other relevant sites

 Genes

Information on a specific gene

This page offers the following options:

• Get mapped sites: same as above.
• Get putative sites: lists all putative sites in the gene, i.e., sites that have sequence similarity with a factor's binding sites. The location and sequence of the site, along with the putative factor's name, is displayed.
• Get intergenic region: displays the sequence of the region upstream of the gene, up to the start (or end) of the next gene.
• Retrieve sequence: displays the sequence of the gene.

 Regulatory elements and transcription factors

This page offers the following options:

• Get factor and element list: this is the table of all known factors, displayed by default.
• Get consensus list: this is a list of all known factor consensi. Each entry is a (factor, consensus sequence) pair.
• Get matrix list: this is a list of all known factor weight matrices. Each entry is a (factor, weight matrix) pair.
• Get distribution of mapped sites: link does not work.
• Get summary of distribution: Tabulates the number of occurrences of each factor in the genome.
• Get correlation between factors: This is a table that tabulates highly correlated factor pairs, i.e., pairs of factors that tend to occur together more often than not.

Information on a specific factor

• Get regulated genes: lists the genes that are regulated by this factor. Each gene is a hyper-link to information about that gene (see above for its format)
• Get sites: lists the sites where this factor binds in the regulated genes.
• Get consensus: retrieves the consensus sequence of the factor's binding site, if known.
• Get matrix: retrieves the weight matrix describing the factor's binding sites, if applicable.
• Get affinity data: displays the binding affinity of the factor to each of its binding sites.
• Get genomewise distribution: lists all occurrences of this factor, along with the name of the gene and the location and sequence of the binding site.
• Sort by copy No.: sorts the genes regulated by this factor, by the number of copies of its binding site in the genes.
• Sort by function category: sorts the genes regulated by this factor, by the regulatory function.

Analysis tools

•  Retrieve promoter sequence: allows retrieval of the upstream region of a gene. The boundaries of the region can be specified.
•  Search existing motif:  determines whether a sequence pattern (motif) occurs in the binding sites of the known factors. The searched motif could be up to 20 characters long, and allows spacers ('N') also. Optional approximate matching that tolerates up to a specified number of mismatches is also possible.
• Search putative regulatory elements: determines if an input sequence (in FASTA format) has putative occurrences of some motif
•  Using predefined matrix and consensus  the motif that is searched is one of the known factor consensi or weight matrices in the database.
•  Using self-defined consensus: the motif that is searched is a user-specified sequence, along with a parameter for allowing mismatches.
•  Using self-defined matrix: the motif that is searched is a user-specified weight matrix.
•  Group genes according to function categories: a set of user-specified genes (by name) are grouped by their function categories.
•  Repetitive sequence analyzer: this is a javascript tool that finds repetitive elements (whose nature can be specified in detail by the user) in a set of user-specified sequences. The page gives very clear instructions on how to use the tool.
• Motif (>6-mer) distribution: this provides a chromosome-wise search for a user-specified motif. The result can be displayed according to the genomic location or the location in the upstream regions of genes.
•  K-tuple relative information: "The k-tuple relative information between two sequences is defined as the log[(n1+1)/(n1+n2+2)], where n1 is the number of k-tuples present in the first sequence while n2 is the number in the second sequence. ". Given two user-specified  sequences (in FASTA format), it computes the above statistic for these two sequences (for a user-specified tuple length). The biological relevance of this statistic is unclear.
•  Palindrome sequences: this is a javascript tool that searches for palindromic substrings in an input sequence (in raw data format). Detailed instructions for using this tool are available on this page.
•  Multisequence alignment by GibbsDNA: this is a tool for multiple sequence alignment by GibbsDNA. The tool is heavily parameterized, so the alignment can be appropriately fine-tuned.

Submit a record to SCPD

• Submit a gene record: allows user to submit information about a gene, such as name, ORF, coordinates, sequence, orientation, reference etc.
• Submit a consensus record: allows user to submit a consensus sequence for a factor, along with its name and reference.
• Submit a matrix record: allows user to submit the weight matrix for a factor.

Documentation

Collection of binding affinity and expression data

Links