Locus Field Format On Genbank
1
1
Entering edit mode
13.7 years ago
Anima Mundi ★ 2.9k

Hello,

I would like to know how the string of the field "LOCUS" on a Genbank (and other similar) entry is formed, and how to read its information. For example: what does NM stand for? What about the XR or XM entries? How do the number following the letters is obtained?

genbank format • 7.1k views
ADD COMMENT
7
Entering edit mode
13.7 years ago
Bio_X2Y ★ 4.4k

The meaning of the LOCUS field is described here

The NM and XM entries, etc., are RefSeq identifiers rather than GenBank identifiers. RefSeq is effectively a well-curated subset of GenBank.

This page explains the meanings of the various prefixes.

ADD COMMENT
0
Entering edit mode

Thanks. Please, can you tell me wich of them are recognized as valid entries in UCSC Genome Browser?

ADD REPLY
0
Entering edit mode

What do you mean by "recognized as valid entries"? If you are asking what can be entered in the "position or search term box", I don't know - it depends on whatever search algorithm UCSC uses. If you need to know, I suggest you open a new question. If you are asking which RefSeq entries are used in the UCSC annotation (which is one of the annotations visible in the browser), I think only the NM and NR entries are used (since the following SQL statement on the UCSC database returns only NM and NR: select mid(mrna,1,2), count(*) from kgxref where mid(mRNA,3,1)="_" group by 1;)

ADD REPLY
0
Entering edit mode

What do you mean by "recognized as valid entries"? If you are asking what can be entered in the "position or search term box", I don't know - it depends on whatever search algorithm UCSC uses. If you need to know, I suggest you open a new question. If you are asking which RefSeq entries are used to create the UCSC annotation (which is one of the annotations visible in the browser), I think only the NM and NR entries are used. Again, if you need to know, I suggest you open a new question.

ADD REPLY
0
Entering edit mode

What do you mean by "recognized as valid entries"? If you are asking what can be entered in the "position or search term box", I don't know - it depends on whatever search algorithm UCSC uses. If you want more details, I suggest you open a new question.

ADD REPLY
0
Entering edit mode

You are right, I should open another question. Thanks again.

ADD REPLY

Login before adding your answer.

Traffic: 2229 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6