• February 23, 2024

FAQ

LGICdb FAQ

I want to quote this database. What is the correct way?
The LGIC Database is not complete. An entry contains mistakes.
How is the name of each entry constructed?
How is the selection between several redundant entries present in the general purpose databases made?
A transcript sequence is presented in the LGIC Database, but I can find only the gene sequence in the other databases.
The gene sequence found in the LGIC Database does not correspond at all to those present in the other databases.
How are the alignments constructed?
What are the planned evolutions of the LGIC Database?
What is the structure of the LGIC Database?

I want to quote this database. What is the correct way?

If you use items coming from this site, please quote one of these papers:

Nicolas Le Novère and Jean-Pierre Changeux (1999). The Ligand-Gated Ion Channel database. Nucleic Acid Research, 27: 340-342.
[PDF version]
Nicolas Le Novère and Jean-Pierre Changeux (2001). LGICdb: the ligand-gated ion channel database. Nucleic Acids Research 29: 294-295.
[PDF version]
Marco Donizelli, Marie-Ange Djite, Nicolas Le Novère (2006). LGICdb: A manually curated sequence database after the genomes. Nucleic Acids Research 34: D267-D269.
[Open Access Version]

The LGIC Database is not complete. An entry contains mistakes.

You can contribute to the completeness of the LGIC Database with new entries or corrections. Feel free to send an e-mail with an accession number or a sequence, or any kind of suggestion, comment, or criticism. Or even better, build your own LGIC Database entries.

How is the name of each entry constructed?

The subunits are named according to the following terminology:
LLLnnnss
where:
LLL: Three characters for the endogenous ligand of the receptor containing the subunit:

ACH acetylcholine
ATP adenosine triphosphate
5HT serotonin
GAB GABA (g-amino butyric acid)
GLU glutamate
GLY glycine
HIS histamine
nnn: The usual name of the subunit.

ssss: A four-letters abbreviation of the linnean denomination of the species from which the subunit was cloned. The first two letters characterize the genus, the last two letters characterize the species. If the last two letters are sp, the species is unknown.

acdo Acheta domesticus (house cricket)
aeae Aedes ægypty (mosquito)
anpl Anas platyrhynchos (duck)
anpl Anopheles gambiae (mosquitp)
apca Aplysia californica (sea hare)
apgo Aphis gossypii (cotton aphid)
aple Apteronotus leptorhynchus (electric fish)
apme Apis meliffera (honey bee)
assu Ascaris suum (nematode)
arth Arabidopsis thaliana (mouse-ear cress)
bota Bos taurus (cow)
caau Carassius auratus (goldfish)
ceca Ceratitis capitata (Mediterranean fruit fly)
cael Cænorhabditis elegans (nematode)
cafa Canis familiaris (dog)
capo Cavia porcellus (guinea-pig)
coli Columba livia (rock pigeon)
drme Drosophila melanogaster (fruitfly)
daae Danio aequipinnatus (zebrafish)
dare Danio rerio (zebrafish)
gaga Gallus gallus (chick)
haco Hæmonchortus contortus (nematode)
hosa Homo sapiens (human)
hevi Heliothis virescens (Tobacco budworm)
lomi Locusta migratoria (locust)
lyst Lymnea stagnalis (pond snail)
moam Morone americana (white perch)
moch Morone chrysops (white perch also …)
mamu Macaca mulatta (rhesus monkey)
mase Manduca sexta (butterfly)
mumu Mus musculus (mouse)
mupu Mustela putorious (ferret)
mype Myzus persica (greenfly)
naha Naja haje (cobra)
nana Naja naja (cobra)
nate Natrix tessellata (watersnake)
onvo Onchocerca volvulus (nematode)
orcu Oryctolagus cuniculus (rabbit)
osci Ostertagia circumcincta (synonymous to Teladorsagia circumcincta)
ormo Oreochromis mossambicus (Mozambique tilapia – bony fish)
orni Oreochromis niloticus (Nile tilapia – bony fish)
rano Rattus norvegicus (rat)
rapi Rana pipiens (frog)
rara Rattus rattus (rat)
scgr Schistocerca gregaria (grasshopper)
scma Schistosoma mansoni (flatworm)
seof Sepia officinalis (cuttlefish)
susc Sus scrofa (pig)
taru Takifugu rubripes (Fugu)
toca Torpedo californica (…)
toma Torpedo marmorata (…)
trco Trichostrongylus colubriformis (nematode)
xela Xenopus lævis (African clawed frog)

How is the selection between several redundant entries present in the general purpose databases made?

It is common to find redundant entries in the general purpose databases. In such a case, I try to keep the bigger clone, assuming that it could contain interesting regulatory sites. Sometimes I fuse several clones in order to get the longest piece. I nevertheless quote the autors of every clone I got. However, I cannot be aware of everything about the field. If you think I made a mistake in my choices, please feel free to communicate me your views.

A transcript sequence is presented in the LGIC Database, but I can find only the gene sequence in the other databases.

When the description of the gene structure is present in the database (determined experimentally or automatically), I reconstruct the (putative) transcript sequence (while still presenting the whole gene sequence anyway).

The gene sequence found in the LGIC Database does not correspond at all to those present in the other databases.

In the case of genomic sequences the gene is sometimes coded on the complementary strand and not on that presented in the databases. In such a case, we “reverse-complement” the sequence to present the coding strand in the LGIC Database.

How are the alignments constructed?

Alignments are performed with the programs ClustalW:

Thompson, J.D., Higgins, D.G. and Gibson, T.J. (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties and weight matrix choice. Nucleic Acids Research, 22:4673-4680.
The default parameters are used.

What are the planned evolutions of the LGIC Database?

The database will of course be completed. Due to the high throughput sequencing of the various genome projects, it is more and more difficult for me to be up-to-date. If you think you are an expert of one of the superfamilies of LGIC, I will be pleased to give you the management of this group of entries. In particular, I would be delighted if somebody would accept to develop new branches about the intracellularly activated LGIC (cyclic nucleotid receptors, IP3 receptors, and so on).

What is the structure of the LGIC Database?

Each entry is stored in an XML file. All the files are then processed automatically to generate the web interface and the search facilities. You can consult the LGICdb XML schema.