Examples of input sequences in FASTA format

The first eight  fields of GFF (General Feature Format) and GTF (Gene Transfer Format) are the same. For more information on GFF/GTF format, refer to http://www.sanger.ac.uk/Software/formats/GFF and  http://genes.cs.wustl.edu/GTF2.html.

Here is a brief description of the GFF/GTF fields:

1. seqname - The name of the sequence.
2. source - The program that generated this feature.
3. feature - The name of this type of feature. The feature type of coding exons must be  "CDS".
4. start - The starting position of the feature in the sequence. The first base is numbered 1.
5. end - The ending position of the feature.
6. score - A score between 0 and 100, or '.' (for don't know/don't care).
7. strand - Valid entries include '+', '-'.
8. frame - If the feature is a coding exon, frame should be a number between 0-2 that represents the reading frame of the first base.

Example 1:

HSCKIIBE	GeneAlgin	CDS	1634	1705	.	+	0
HSCKIIBE	GeneAlign	CDS	2672	2774	.	+	0
HSCKIIBE	GeneAlign	CDS	3344	3459	.	+	2
HSCKIIBE	GeneAlign	CDS	3906	3981	.	+	0
HSCKIIBE	GeneAlign	CDS	4128	4317	.	+	2
HSCKIIBE	GeneAlign	CDS	4645	4735	.	+	1

Example 2:

Mm.4.ENSMUST30521.1	EnsEMBL	exon	137143182	137143929	.	-	.
Mm.4.ENSMUST30521.1	EnsEMBL	CDS	137143182	137143901	.	-	0
Mm.4.ENSMUST30521.1	EnsEMBL	start_codon	137143899	137143901	.	-	0
Mm.4.ENSMUST30521.1	EnsEMBL	exon	137131214	137131372	.	-	.
Mm.4.ENSMUST30521.1	EnsEMBL	CDS	137131214	137131372	.	-	0
Mm.4.ENSMUST30521.1	EnsEMBL	exon	137130549	137131003	.	-	.
Mm.4.ENSMUST30521.1	EnsEMBL	CDS	137130563	137131003	.	-	0
Mm.4.ENSMUST30521.1	EnsEMBL	stop_codon	137130560	137130562	.	-	0

　

Example 1 (multi-exon gene): human.fasta mouse.fasta m_anno.txt (Output)

Example 2 (multi-exon gene): human.fasta mouse.fasta m_anno.txt (Output)

Example 3 (multi-exon gene): human.fasta mouse.fasta m_anno.txt (Output)

Example 4 (include initial micro_exon): human.fasta mouse.fasta m_anno.txt (Output)

Example 5 (include internal micro_exon): human.fasta mouse.fasta m_anno.txt (Output)

Example 6 (include terminal micro_exon): human.fasta mouse.fasta m_anno.txt (Output)

Example 7 (single-exon gene): human.fasta mouse.fasta m_anno.txt (Output)

Example 8 (predict on mouse sequence): mouse.fasta human.fasta h_anno.txt (Output)
　

A number of files will be created by GeneAlign.

result.htm - include coding exon annotation for first DNA sequence and links of results

result.gff - a text file  in GFF format  for coding exon annotation of first DNA sequence

alignment.htm - coding exon alignments

browser.txt (optional) - a text file for being loaded by UCSC Genome Browser.

Incorrect output on the UCSC Genome Browser :

the first sequence is not retrieved on the forward strand : The output would be reverse. Try to retrieve sequence from the "Get DNA in Window" page of the UCSC Genome Browser.

the first human sequence is not retrieved from the Human May 2004 (hg17) assembly :  The output would be shift.

the first mouse is not retrieved from the Mouse Aug. 2005 (mm7) assembly  :  The output would be shift.

the sequence is inconsistent with CDS annotation: Try to retrieve sequence from the "Get DNA in Window" page of the UCSC Genome Browser.

Where you can find "Get DNA in Window" page : An example of "Get DNA in Window" page - retrieve.pdf.

 No significant alignment:

Genes on the reverse strand : Try to add the word "reverse" on the description line at the field "strand_for_prediction" for the first sequence and run GeneAlign again. The default strand for prediction is on the forward stand.

Gene annotation and the second sequence are inconsistent.

Highly dissimilar gene structures between input sequences : GeneAlign is currently requiring similar gene structures in the input sequences, some exons will be missed by the program if the structures are high dissimilar.