http://gmod.org/wiki/GFF

gff介绍

GFF3: http://song.sourceforge.net/gff3.shtml

GFF: http://www.sanger.ac.uk/Software/formats/GFF/

GFF2PS: http://genome.imim.es/software/gfftools/GFF2PS.html

http://gmod.org/wiki/GBrowse

GBrowse

http://xerad.systemsbiology.net/MotifMogulServer/MotifMogulFAQ.html

PSL

format

PSL lines represent alignments, and are typically taken from

files generated by BLAT or psLayout. See the BLAT documentation for more details. All of the

following fields are required on each data line within a PSL

file:

matches - Number of bases that match that

aren't repeats

misMatches - Number of bases that don't

match

repMatches - Number of bases that match but

are part of repeats

nCount - Number of 'N' bases

qNumInsert - Number of inserts in query

qBaseInsert - Number of bases inserted in

query

tNumInsert - Number of inserts in target

tBaseInsert - Number of bases inserted in

target

strand - '+' or '-' for query strand. For

translated alignments, second '+'or '-' is for genomic strand

qName - Query sequence name

qSize - Query sequence size

qStart - Alignment start position in

query

qEnd - Alignment end position in query

tName - Target sequence name

tSize - Target sequence size

tStart - Alignment start position in

target

tEnd - Alignment end position in target

blockCount - Number of blocks in the alignment

(a block contains no gaps)

blockSizes - Comma-separated list of sizes of

each block

qStarts - Comma-separated list of starting

positions of each block in query

tStarts - Comma-separated list of starting

positions of each block in target

Example:

Here is an example of an annotation track in PSL format. Note that

line breaks have been inserted into the PSL lines in this example

for documentation display purposes. Click here for a copy of this example that can be pasted into the

browser without editing.

track name=fishBlats description="Fish BLAT" useScore=1

59 9 0 0 1 823 1 96 +- FS_CONTIG_48080_1 1955 171 1062 chr22

47748585 13073589 13073753 2 48,20, 171,1042,

34674832,34674976,

59 7 0 0 1 55 1 55 +- FS_CONTIG_26780_1 2825 2456 2577 chr22

47748585 13073626 13073747 2 21,45, 2456,2532,

34674838,34674914,

59 7 0 0 1 55 1 55 -+ FS_CONTIG_26780_1 2825 2455 2676 chr22

47748585 13073727 13073848 2 45,21, 249,349, 13073727,13073827,

Be aware that the coordinates for a negative strand in a PSL

line are handled in a special way. In the qStart and

qEnd fields, the coordinates indicate the position where

the query matches from the point of view of the forward strand,

even when the match is on the reverse strand. However, in the

qStarts list, the coordinates are reversed.

Example:

Here is a 30-mer containing 2 blocks that align on the minus strand

and 2 blocks that align on the plus strand (this sometimes can

happen in response to assembly errors):

0 1 2 3 tens position in query

0123456789012345678901234567890 ones position in query

++++ +++++ plus strand alignment on query

-------- ---------- minus strand alignment on query

Plus strand:

qStart=12

qEnd=31

blockSizes=4,5

qStarts=12,26

Minus strand:

qStart=4

qEnd=26

blockSizes=10,8

qStarts=5,19

Essentially, the minus strand blockSizes and

qStarts are what you would get if you reverse-complemented

the query. However, the qStart and qEnd are not

reversed. To convert one to the other: qStart = qSize - revQEnd

qEnd = qSize - revQStart

GFF format

GFF (General Feature Format) lines are based on the GFF standard

file format. GFF lines have nine required fields that must

be tab-separated. If the fields are separated by spaces instead of

tabs, the track will not display correctly. For more information on

GFF format, refer to http://www.sanger.ac.uk/Software/formats/GFF.

Here is a brief description of the GFF fields:

seqname - The name of the sequence. Must be a

chromosome or scaffold.

source - The program that generated this

feature.

feature - The name of this type of feature.

Some examples of standard feature types are "CDS", "start_codon",

"stop_codon", and "exon".

start - The starting position of the feature

in the sequence. The first base is numbered 1.

end - The ending position of the feature

(inclusive).

score - A score between 0 and 1000. If the

track line useScore attribute is set to 1 for this

annotation data set, the score value will determine the

level of gray in which this feature is displayed (higher numbers =

darker gray). If there is no score value, enter ".".

strand - Valid entries include '+', '-', or

'.' (for don't know/don't care).

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. If the feature is not a coding

exon, the value should be '.'.

group - All lines with the same group are

linked together into a single item.

Example:

Here's an example of a GFF-based track. Click here for a copy of this example that can be pasted into the

browser without editing. NOTE: Paste operations on some operating

systems will replace tabs with spaces, which will result in an

error when the GFF track is uploaded. You can circumvent this

problem by pasting the URL of the above example

(http://genome.ucsc.edu/goldenPath/help/regulatory.txt) instead of

the text itselfinto the custom annotation track text box.

track name=regulatory description="TeleGene(tm) Regulatory

Regions"

chr22 TeleGene enhancer 1000000 1001000 500 + . touch1

chr22 TeleGene promoter 1010000 1010100 900 + . touch1

chr22 TeleGene promoter 1020000 1020000 800 - . touch2

GTF

format

GTF (Gene Transfer Format) is a

refinement to GFF that tightens the specification. The first eight

GTF fields are the same as GFF. The group field has been

expanded into a list of attributes. Each attribute

consists of a type/value pair. Attributes must end in a semi-colon,

and be separated from any following attribute by exactly one

space.

The attribute list must begin with the two mandatory

attributes:

gene_id value - A globally

unique identifier for the genomic source of the sequence.

transcript_id value - A

globally unique identifier for the predicted transcript.

Example:

Here is an example of the ninth field in a GTF data line:

gene_id

"Em:U62317.C22.6.mRNA"; transcript_id "Em:U62317.C22.6.mRNA";

exon_number 1

For more information on this format, see http://genes.cse.wustl.edu/GTF2.html.

The Genome Browser groups together GTF lines that have the same

transcript_id value. It only looks at features of type

exon and CDS.