GABOS/GAFEP - Get A Bit Of Sequence/Get A Few Exon Primers

GABOS (Get A Bit Of Sequence). Select Genome: then select a Sequence Object below:

Check one or more Annotation Files to use:

Either enter a list of gene names OR

Select chromosome name and enter a sequence range.

Enter a comma separated list of Gene Names:
Eg. NM_025446, NM_008413, BC064047, chr1.64

Use Regular Expression test for Gene Names.

Specify a genetic element and sequence range.
Select the Genetic Element :
Specify the Sequence Range:
Note: 5.67m = 5,670,000, 4M = 4 million, 500k = 500,000

Specify Sequence to retrieve.

Both strands. Only Plus strand. Only Minus strand.

Upstream Bases: Downstream Bases:

Put Limits on Sequence to retrieve.

Base Range Selection:For Exons,Introns,UTR's & Genomic Seq.
"e" = end base. "1-e" = All bases, "1-20"= first 20 bases
"30-e" = base no. 30 to last base. "e/2-e" = last half of bases.

Object Range Selection for Exons and Introns :
"e" = end exon/intron. "1-e" = All exons/introns.
"1" = first, "2-e" = all but the first, "e/2-e" = last half of objects.

Specify Sequence Output Options:

Select character to seperate fields on the Fasta Description Line. Space( ) Semi Colon(;) Star(*) Comma(,) Tilda(~)	Fasta line length:	Limit No. of bases/object:
String of characters to be inserted BEFORE each DNA object. String of characters to be inserted AFTER each DNA object.	Do NOT display Sequence Data. Do NOT display Fasta Description Lines. Concatenate ALL Sequences. Concatenate ONLY Sequence from each DNA object.

GAFEP (Get a Few Exon Primers) Parameters

5'Primer : Cushion : Exon Min : Opt : Max : Overlap : Cushion : 3'Primer :

Percentage adjustment: The Primer Area is adjusted by this percentage for segments of large Exons that are split.[1-100].

GAFEP Upstream sequence: The default = 5'Primer Area + 5'Cushion + (Exon Minimum)/2.

GAFEP Downstream sequence: The default = (Exon Minimum)/2 + 3'Cushion + 3'Primer Area.

Request version information here:

GABOS/GAFEP Documentation