Name

withncbi - egaz and alignDB work with external (NCBI/EBI) data.

Purpose

Fetch sequences, generate reports and build alignments according to various NCBI databases.

For more detailed, check README.md in each sub-directories.

Directory organization

db/: turn NCBI genome reports and assembly reports into a query-able MySQL database.
ensembl/: Ensembl related scripts.
misc/: miscellaneous projects.
pop/: build alignments on an whole Eukaryotes genus.
taxon/: process (small) genomes according to NCBI Taxonomy.
util/: miscellaneous utilities.

Conventions

fasta

.fa - genomic sequences
.fas - blocked fasta files
.fasta - normal/miscellaneous fasta files

fastq

Use .fq over .fastq

Concepts

IntSpans

An IntSpan represents sets of integers as a number of inclusive ranges, for example '1-10,19,45-48'.

The following picture is the schema of an IntSpan object. Jump lines are above the baseline; loop lines are below it.

AlignDB::IntSpan and jintspan are implements of IntSpan objects in Perl and Java, respectively.

Positions

Examples in S288c.txt

I:1-100
I(+):90-150
S288c.I(-):190-200
II:21294-22075
II:23537-24097

Simple rules:

chromosome and start are required
species, strand and end are optional
. to separate species and chromosome
strand is one of + and - and surround by round brackets
: to separate names and digits
- to separate start and end
names should be alphanumeric and without spaces

species.chromosome(strand):start-end
--------^^^^^^^^^^--------^^^^^^----

Runlists in YAML

App::RL

jrunlist

Blocked fasta files

Examples in example.fas

>S288c.I(+):13267-13287|species=S288c
TCGTCAGTTGGTTGACCATTA
>YJM789.gi_151941327(-):5668-5688|species=YJM789
TCGTCAGTTGGTTGACCATTA
>RM11.gi_61385832(-):5590-5610|species=RM11
TCGTCAGTTGGTTGACCATTA
>Spar.gi_29362400(+):2477-2497|species=Spar
TCATCAGTTGGCAAACCGTTA