Locus Field Format On Genbank
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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
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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.

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

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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;)

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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.

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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.

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

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