Database

• The chromosome files
• The .config file

To design fluorescence in situ hybridization (FISH) probes, ifpd selects sets of sequences from databases of oligonucleotide sequences, which are designed to hybridize to a single genomic locus with high specificity at certain FISH conditions.

In ifpd, each database consist of a folder with one file per chromosome (or feature, i.e., there is no requirement for a file name to start with “chr”), and a .config file. In other words, the content of a database folder will be something like the following example.

database_folder
    ┣ chr1
    ┣ chr2
    ┣ ...
    ┣ chrN
    ┗ .config

To see how to generate a database, check the ifpd_mkdb script description.

The chromosome files

Each chromosome file is a plain text file containing three (3) columns: start, end, and sequence (the latter contains the sequence corresponding to the start-end region). Please, note that start and end position are expected to respect follow the UCSC BED file format, i.e.:

• start: the starting position of the feature in the chromosome. The first base in a chromosome is numbered 0. The start position in each BED feature is therefore interpreted to be 1 greater than the start position listed in the feature. For example, start=9, end=20 is interpreted to span bases 10 through 20, inclusive.
• end: the ending position of the feature in the chromosome . The end position in each BED feature is one-based. Hence, the end base is not included in the display of the feature. For example, the first 100 bases of a chromosome are defined as start=0, end=100, and span the bases numbered 0-99.

It is of interest to note that, at the moment of generation, it is possible to retain in the database any number of additional columns, which are anyhow not used by the ifpd package.

The .config file

The .config file is automatically generated alongside a database. It is used for compatibility with the whole ifpd package, and to validate a newly generated databases.

This file tracks a number of features and parameters of the database, alongside custom ones that the user can add when generating it. An example of .config file is the following:

[DATABASE]
name = databaseName
refgenome = hg19

[OLIGOS]
min_dist = 10
min_length = 40
max_length = 40
overlaps = False

[SOURCE]
bed = /media/test/MYC.bed
enforced2bed3 = False
outdirectory = /media/test/MYC

[CUSTOM]
url = example.com

Here is the meaning of each field:

• DATABASE
  • name: name of the database, used by the web interface.
  • refgenome: reference genome, for trackability purposes.
• OLIGOS
  • min_dist: minimum distance between consecutive oligos (end of the first, start of the second).
  • min_length, max_length: oligos length range.
  • overlaps: whether the database contains overlapping oligos.
• SOURCE
  • bed: the input BED-like file used to generate the database with ifpd_mkdb.
  • enforced2bed3: whether the input BED-like file was forced to BED3 format.
  • outdirectory: database directory.
• CUSTOM
  • Any custom field added by the user will/should be stored here.