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

Exon.	Intron.	5'UTR.	CDS.	3'UTR.	Transcript.	GenomicSeq.	DNA.

Check one or more Annotation Files to use:

Annotation File Information  On the UCSC help page, Select the group and track and then click the describe table schema button.

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     : All Chromosomes 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:

The Percentage Up/Down or Extra bases added are additional to the corresponding No. of Upstream or Downstream Bases specified above.
%UpStream.	%DownStream.	Extra Bases Up.	Extra Bases Down.	Do not Enter Next or Previous Object.
Do not add Percentage bases before the first exon/intron or after the last exon/intron:				.

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