{"id":333,"date":"2016-12-12T17:10:52","date_gmt":"2016-12-13T01:10:52","guid":{"rendered":"http:\/\/genome.ucsc.edu\/blog\/?p=333"},"modified":"2021-10-30T22:15:53","modified_gmt":"2021-10-30T22:15:53","slug":"the-ucsc-genome-browser-coordinate-counting-systems","status":"publish","type":"post","link":"https:\/\/genome-blog.gi.ucsc.edu\/blog\/2016\/12\/12\/the-ucsc-genome-browser-coordinate-counting-systems\/","title":{"rendered":"The UCSC Genome Browser Coordinate Counting Systems"},"content":{"rendered":"

If you think dogs can’t count, try putting three dog biscuits in your pocket and then giving Fido only two of them.  <\/span><\/i><\/span><\/p>\n

~Phil Pastoret<\/span><\/i><\/span><\/p>\n

\u201cCounting is easy. Right?\u201d<\/p>\n

I say this with my hand out, my thumb and 4 fingers spread out. With my other hand’s pointer finger, I simply count each digit, “one, two, three, four, five.” Easy.<\/p>\n

But what happens when you start counting at 0 instead of 1? You can see that you have 5 digits (4 fingers and a thumb), but how do you calculate the size of your range?<\/p>\n

With your hand in mind as an example, let’s look at counting conventions as they relate to bioinformatics and the UCSC Genome Browser genomic coordinate systems.<\/p>\n

The UCSC Genome Browser uses two different systems:<\/p>\n

\r\n
\r\n \u201c1-start, fully-closed\u201d = coordinates positioned within the web-based UCSC Genome Browser. \u201c0-start, half-open\u201d = coordinates stored in database tables.\r\n <\/div>\r\n <\/div>\n
Table 1. UCSC Genome Browser coordinate systems summary<\/span>
\n<\/b><\/span><\/h5>\n\n\n\n\n\n\n
0-start, half-open (0-based)<\/b><\/td>\n1-start, fully-closed (1-based)<\/b><\/td>\n<\/tr>\n
“BED” format (Browser Extensible Data):<\/span>
\nchr1 12714000<\/span>0<\/strong> 127140001
\nNote: Spaces, not punctuation
\nWhen using BED format, browser & utilities<\/em><\/span>
\nassume coords are 0-start, half-open.<\/em><\/span><\/span><\/span><\/td>\n		“Position” format:<\/span>
\nchr1:<\/span><\/strong>12714000<\/span>1-<\/span><\/strong>127140001
\nNote: Punctuation used, no spaces
\nWhen using “position” format, browser & utilities<\/em><\/span>
\nassume coords are 1-start, fully-closed.<\/em><\/span><\/span><\/td>\n<\/tr>\n
Stored in UCSC Genome Browser tables<\/span><\/td>\nPositioned in UCSC Genome Browser web interface<\/span><\/td>\n<\/tr>\n
To convert to 1-start, fully-closed:<\/span>
\nadd 1 to start, end = same<\/span><\/td>\n		To convert to 0-start, half-open:
\nsubtract 1 from start, end = same<\/span> <\/span><\/i><\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n

Section 1: Interval types<\/strong><\/span><\/h1>\n

0-start vs. 1-start<\/b> : <\/span>Does counting start at 0 or 1?
\n<\/span>Synonyms:
\nSometimes referred to as \u201c0-based” vs “1-based\u201d or <\/span>“0-relative vs “1-relative.”<\/span><\/p>\n

Interval Types
\n<\/b><\/span>For a counted range, is the <\/span>specified interval<\/b> fully-open<\/span>, <\/span>fully-closed<\/span>, or a <\/span>hybrid-interval (e.g., half-open)<\/span>? <\/span><\/span><\/p>\n

Ok, time to flashback to math class!
\nYou might recall that specifying an interval type as open, closed (or a combination, e.g., \u201chalf-open\u201d) refers to whether or not the endpoints of the interval are included in the set. For further explanation, see the<\/span>interval math terminology wiki article<\/span><\/a>. <\/span>Figure 1<\/b> below describes various interval types.
\n<\/span>
\n\"Figure1\"<\/a><\/p>\n

Figure 1.<\/b> (To enlarge, click image.) Description of interval types. <\/span><\/i><\/p>\n

Section 2: Interval types in the UCSC Genome Browser<\/span>
\n<\/b><\/span><\/h1>\n

UCSC Genome Browser web interface = \u201c1-start, fully-closed\u201d<\/b><\/span><\/h2>\n

A common counting convention is a system that we all used when we first learned to count the fingers on our hands; this is referred to as the “one-based, fully-closed” system (<\/span>Figure 2<\/b>, below). Note that an extra step is needed to calculate the range total (5). <\/span><\/p>\n

The <\/span>\u201c1-start, fully-closed\u201d system is what you SEE when using the UCSC Genome Browser web interface. However, all positional data that are stored in database tables use a different system. <\/span><\/p>\n

\"1-starthandfinal\"<\/a><\/p>\n

Figure 2. <\/b>(To enlarge, click image.)<\/span> 1-start, fully-closed interval. Most common counting convention. Used within the UCSC Genome Browser web interface (but not used in UCSC Genome Browser databases\/tables). We calculate that we have 5 digits because 5 (pinky finger, range end) – 1 (the thumb, range start) = 4. We then need to add one to calculate the correct range; 4+1= 5.<\/span><\/i><\/p>\n

UCSC Genome Browser tables = \u201c0-start, half-open\u201d<\/b><\/span><\/h2>\n

While the commonly-used “one-start, fully-closed” system is more intuitive, it is not always the most efficient method for performing calculations in bioinformatic systems, because an additional step is required to calculate the size of the base-pair (bp) range. <\/span><\/p>\n

To increase efficiency, the UCSC Genome Browser uses a \u201chybrid-interval\u201d coordinate system for storing coordinates in databases\/tables that is referred to as \u201c0-start, half-open\u201d (see <\/span>Figure 3<\/b>, below). <\/span><\/p>\n

Although coordinates in the web browser are converted to the more human-readable \u201c1-start, fully-closed\u201d system, coordinates are stored in database tables as \u201c0-start, half-open.\u201d You may have heard various terms to express this 0-start system:<\/span><\/p>\n

Synonyms for \u201c0-start, half-open\u201d<\/b><\/span><\/p>\n