Decoding EST names

We have tried to encode as much information as is possible in the names of our EST clones. This has perhaps made the names a little unwieldy, but we hope that the added information is useful to the community. To aid in decoding the names, here's a quick guide.

AS3ISA007 is a third stage infective larval, full length cDNA from the Scott/Blaxter labs.

The sequence derived from this clone has an additional two letter suffix indicating which primer was used in sequencing.

Each EST clone has a nine or ten character name which is split up as follows:

AS3ISA007

The first two letters indicate the laboratory originating the clone or sequence:

SW= Steve Williams
KJ= Kunthala Jayaraman
RR= Reda Ramzy
AS= Alan Scott
MB= Mark Blaxter
TN= Tom Nutman
GW= Gary Weil

These are the people to contact if you want the clone or more information

AS3ISA007

The next three letters indicate which library the clone came from, and is a useful way of checking the stage specificity of any particular gene

MFC= microfilariae, conventional library
2SL= second stage mosquito-derived larvae, SL-dT RT-PCR library
3IS= third stage infective mosquito-derived larvae, SL-dT RT-PCR library
3IC= third stage infective mosquito-derived larvae, conventional library
4SL= fourth stage jird-derived larvae, SL-dT RT-PCR library
AFC= adult females, conventional library
MFC= adult males, conventional library

The SL-dT RT-PCR constructed libraries contain full length SL-dT cDNAs. The conventionally constructed libraries cannot be guaranteed to contain full length transcripts, but we do see a significant number of SL1 fragments at the exterme 5' ends, suggesting that the libraries are of uniformly high quality. The conventional libraries will contain cDNAs for non-trans-spliced mRNAs.

AS3ISA007

The final four or five characters identify the clone. Different labs have taken different routes for naming: these are outlined below...

Steve Williams' Lab in collaboration with Reda Ramzy's Lab and Barton Slatko's Lab.

The SW and RR clones are numbered sequentially from A001 for each of the three libraries sampled (adult male, microfilaria and L3). The numbering goes A999, A1000, A1001, etc.

Alan Scott's Lab in collaboration with Mark Blaxter's Lab

The Scott/Blaxter lab clones have been numbered with a four character code with different letter prefixes indicating different phases of sequencing:

A001-A099 = pilot sudy on SL-dT L3 library
B001-B399 = SL-dT L3 library main study
C400-C999 = SL-dT L4 library main study

Kunthala Jayaraman's Lab in collaboration with Alan Scott's Lab

The KJ clones are numbered from B001.

Mark Blaxter's lab

The Blaxter lab uses the following coding

D001-D096 = pilot study on SL-dT L4 library

The Blaxter lab is now sequencing from microtitre plate arrayed clones, and is using the well ID as a coding for the clones. We are picking into plates (named E0 through E9, F0 through F9, etc) and adding the row, column naming (A01, A02, A03...etc) thereafter.