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Reptilian Brain Transcriptome
version 1 - September 2011

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Input information

Type
The requested type of data may either focus on: (i) the contigs and the singletons (without microsatellites), (ii) the contigs and the singletons with microsatellites, and (iii) the consensus sequences.
Species
Select one of the four reptilian species sequenced in this project, or the chicken transcriptome that was used as a reference.
Information Requested
The user may choose to display (i) only the sequence names, (ii) the sequence names and the corresponding sequences, or (iii) all the available information based on the other selections made.

Contigs and Singletons

Length
The desired length of the contigs and singletons may be definited.
Reads
The number of reads comprised in a contig is choosen. If the number of reads is equal to one, then only singletons are displayed, whereas if it is set to greater than one, only information on contigs is provided.
mtDNA
The selected sequences may be (true) or not (false) part of the mitochondrial genome. Otherwise, this information may be ignored (not considered).
Microsatellites
The user may restrict the query only to contigs containing microsatellites (true).
Microsatellites type
The type of repeat may be defined (all, mono-, di-, tri-, tetra-, penta-, and hexanucleotides). Complex are the microsatellites that are located on the same contig and their distance is less than 50 bases.
Microsatellites size
The size of the repeat may be indicated. In order to obtain the number of repeats, divide the microsatelllite size by the motif length (one for mononucleotides, two for dinucleotides, etc). Mononucleotides were taken into account only when they were repeated more than 10 times, whereas the other types were ignored if they were found less than 5 times.
Microsatellites start
The contig base at which the microsatellite starts.
Microsatellites end
The contig base at which the microsatellite ends. In order to obtain the length of the 3' flanking region, substract the 'microsatellite end' from the contig length.
SNPs
The presence/absence of SNPs in the contigs may be taken into account, or ignored. Note that if the dataset is restricted to sequences having a SNP, then only contigs are displayed. On the other hand, if SNPs are not considered, contigs and singletons can be selected. Only the cases where the 'minor allele' was sequenced more than three times are taken into account.
Indels
The presence/absence of indels in the contigs may be taken into account, or ignored. Note that if the dataset is restricted to sequences having a indel, then only contigs are displayed. On the other hand, if indels are not considered, contigs and singletons can be selected. Only the cases where the 'minor allele' was sequenced more than three times are taken into account.

Consensus

Database
The contigs and singletons were BLASTed against several databases. The user may choose the result of all, or a specific database to be displayed.
Number of sources
A consensus sequence may originate from the alignment of only one contig or singleton against a database sequence (one-to-one consensus with one source), or from the alignment of several congits and/or singletons against a database sequence (one-to-many consensus with more than one sources)
Percentage of gaps
The percentage of gaps in the consensus sequence may be defined. Note that all one-to-one consensus sequences have 0% of gaps, because there is no alignment.
Percentage of Ns/Xs
The percentage of ambiguities (N for nucleotides and X for proteins) may be defined.

Results Page

Summary
A summary of the user's selections is given.
Table
The selected sequences are displayed in a table format, along with the requested data.
Export
An 'Export' button exists at the end of the results page. Once pressed, the displayed table is exported to a CSV file (to be opened with MS Excel, for example).

Upload Page

Contigs and singletons
This page allows the user to obtain all the information available for certain Contigs and/or Singletons, which were the result of a previously performed query, for example. The list of contigs/singletons should be included in a TXT file prepared with a text editor (like TextWrangler) and not XLS.
Consensus
Similar function as for Contigs and Singletons.

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