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**HenryN** · July 19, 2006, 07:23 AM

Re: Rudimentary Gene Sequencing Question(s)

Originally posted by hawkeye

I was looking at a recent post by Niman that included some sequences and I'm curious to know, why isn't there a standard structure for these sequences? Is the structure tied to the date? For instance, it seems the more recent sections of this sequence indicicate the type of animal that its from:
DQ826532 A/mallard/BC/373/2005 2005 H5N2

However, older onese lack that level of clarity.
U53162 A/Wisconsin/4754/94 1994 H1N1

Has anyone written a parser that would place these sequences along a world map? Would that be of any use?

DQ826532 A/mallard/BC/373/2005 2005 H5N2
DQ280250 A/swine/Ontario/11112/04 2004 H1N1
DQ447187 A/swine/Taiwan/CO935/2004 2004 H1N2
DQ431990 A/swine/Taiwan/CO935/2004 2004 H1N2
AY129156 A/Swine/Korea/CY02/02 2002 H1N2
AY233393 A/Duck/NC/91347/01 2001 H1N2
DQ058215 A/swine/Guangdong/2/01 2001 H1N1
AF455682 A/Swine/Illinois/100084/01 2001 H1N2
AF455681 A/Swine/Illinois/100085A/01 2001 H1N2
AF455679 A/Swine/Iowa/930/01 2001 H1N2
AY060050 A/Swine/MN/16419/01 2001 H1N2
AY060048 A/Swine/MN/23124-S/01 2001 H1N2
AY060047 A/Swine/MN/23124-T/01 2001 H1N2
AY060051 A/Swine/MN/34893/01 2001 H1N2
AF455677 A/Swine/North Carolina/93523/01 2001 H1N2
AF455675 A/Swine/Ohio/891/01 HA (4) 2001 H1N2
AF455680 A/Swine/Indiana/P12439/00 2000 H1N2
AF455678 A/Swine/Minnesota/55551/00 2000 H1N2
AF250124 A/Swine/Indiana/9K035/99 1999 H1N2
AF222035 A/Swine/Wisconsin/458/98 1998 H1N1
AF222036 A/Swine/Wisconsin/464/98 1998 H1N1
AF222026 A/Swine/Wisconsin/125/97 1997 H1N1
AF222027 A/Swine/Wisconsin/136/97 1997 H1N1
AF222032 A/Swine/Wisconsin/235/97 1997 H1N1
AF222033 A/Swine/Wisconsin/238/97 1997 H1N1
U53162 A/Wisconsin/4754/94 1994 H1N1
U53163 A/Wisconsin/4755/94 1994 H1N1
S67220 A/Swine/Nebraska/1/92 1992 H1N1
L09063 A/Swine/Nebraska/1/92 1992 H1
L24362 A/Maryland/12/91 1991 H1N1
U46783 A/Swine/Beijing/47/91 1991 H1N1
U11857 A/Swine/St-Hyacinthe/106/91 1991 H1
M81707 A/Swine/Indiana/1726/88 1988 H1N1
DQ508905 A/Wilson-Smith/1933 1933 H1N1
J02176 A/WSN/33 1933 H1N1

Flu isolates are named by convention which has the type, species, location, sample numbber, year of isolation, and sero-type. No listing of species indocates the isolate is human.

An alphabetical list of sequences at GenBank (grouped by sero-type) is here

http://www.ncbi.nlm.nih.gov/Taxonomy...hmode=1&unlock

The list above is by date of isolate (group alphabetically within each year).

There are over 7000 flu isolates at GenBank (and Los Alamos).

**hawkeye** · July 19, 2006, 09:19 AM

Re: Rudimentary Gene Sequencing Question(s)

Thnx Niman for the additional info

I've taken the h5n1 entries that are listed at:
http://www.ncbi.nlm.nih.gov/Taxonomy...hmode=1&unlock

and I've converted them into an xml format.

I was going to write a parser, which I've done, but it's difficult to interpret the data since many entries don't follow the same convention (i.e. two locations etc.).

-hawkeye

Attached Files

sequences_h5n1.zip (5.5 KB, 174 views)

**JJackson** · July 19, 2006, 10:52 AM

Re: Rudimentary Gene Sequencing Question(s)

From a data querying point of view it is a mess.

If the basic structure is

A/species/location/sample no./year Serotype

the only bit that reliably works A (or B or C) pre fix.

Species can be omitted (in humans), a common name (Bar headed geese) or a Latin name. With exceptions even form these 'rules' e.g. Wilson-Smith

Location is often a country but can be a region or town.

Sample no. is often just a sequential no. but some times contains other data like the sampling lab NAMRU2

Even the year varies from yyyy or yy

Serotype format is normally consistent although I have seen it omitted.

All this makes life unnecessarily tricky and is darned right unscientific. An agreed standard with refusal to accept incorrectly 'addressed' submissions would be a good start perhaps with a little more data. method of amplification, culture date etc.

Just a suggestion -

A/homo sapiens/Latitude-Longitude/testing lab/sample no.(sequential numeric only)/amplification (e.g.PCR)/cultured (e.g.MDCK)/mm-yyyy/HxNx ?

On the internet we place RFCs (Request For Comments) all ideas welcome, agree a standard and adopt it

Any one else got suggestions?

**LMonty** · July 19, 2006, 10:57 AM

Re: Rudimentary Gene Sequencing Question(s)

I think its a great idea. Standardization should make for easier database entry and query. Ya gotta like that!

My vote is you go for it. Maybe one or more of the journalists would find such an inititative, especially from a group like ours, to be an interesting topic for an article. That type of exposure might just tip the scales in favor of such a standradization.

**JJackson** · July 19, 2006, 11:16 AM

Re: Rudimentary Gene Sequencing Question(s)

P.S. I know rigid structures have weaknesses and sometimes it will not be possible to tick all the boxes.

For instance I have seen the species type listed as environment (water samples or poultry litter), The Spanish Grebe would have been difficult to pin down to species level. Samples handed in by 'concerned citizens' may present a problem re grid reference.

Following H5N1 has show up some weaknesses in the system e.g. Dates only being held to the year can be frustration is you are trying to follow patterns of mutations along migratory routes (was a sample taken from a migratory bird going to Africa from Asia or returning months later etc.)
In these days of GIS (http://en.wikipedia.org/wiki/GIS) a powerful analysis opportunity is being missed by the vague area classifications, sometimes this is a country covering a sizable chunk of the globe and on other occasions I never worked out what part of the world the sample came from (A/Swine/MN/16419/01 2001 H1N2 Myanmar?).

**LMonty** · July 19, 2006, 11:35 AM

Re: Rudimentary Gene Sequencing Question(s)

JJackson- I think that the place is sometimes a US state, rather than a country name- MN is Maine IIRC. I'm not sure if thats the answer here, just a speculation.

Myanmar is the new name for Burma.

HTH

**Mingus** · July 19, 2006, 11:43 AM

Re: Rudimentary Gene Sequencing Question(s)

Yes, MN is common for strain coming from minesota.

**JJackson** · July 19, 2006, 11:55 AM

Re: Rudimentary Gene Sequencing Question(s)

Minisota or Maine? Anyway if I find initials like that again I will search for US states. With thanks a European.

**LMonty** · July 19, 2006, 11:58 AM

Re: Rudimentary Gene Sequencing Question(s)

LOL, I got that wrong! OK, Minnesota! That just gave me the impetus to look for a chart of the different state abbreviations, in case ots of any help to our readers.

from the US Post Office Site (far more likely to be right than I am!!! LOL)

State Abbreviations

State/Possession
Abbreviation

ALABAMA
AL

ALASKA
AK

AMERICAN SAMOA
AS

ARIZONA
AZ

ARKANSAS
AR

CALIFORNIA
CA

COLORADO
CO

CONNECTICUT
CT

DELAWARE
DE

DISTRICT OF COLUMBIA
DC

FEDERATED STATES OF MICRONESIA
FM

FLORIDA
FL

GEORGIA
GA

GUAM
GU

HAWAII
HI

IDAHO
ID

ILLINOIS
IL

INDIANA
IN

IOWA
IA

KANSAS
KS

KENTUCKY
KY

LOUISIANA
LA

MAINE
ME

MARSHALL ISLANDS
MH

MARYLAND
MD

MASSACHUSETTS
MA

MICHIGAN
MI

MINNESOTA
MN

MISSISSIPPI
MS

MISSOURI
MO

MONTANA
MT

NEBRASKA
NE

NEVADA
NV

NEW HAMPSHIRE
NH

NEW JERSEY
NJ

NEW MEXICO
NM

NEW YORK
NY

NORTH CAROLINA
NC

NORTH DAKOTA
ND

NORTHERN MARIANA ISLANDS
MP

OHIO
OH

OKLAHOMA
OK

OREGON
OR

PALAU
PW

PENNSYLVANIA
PA

PUERTO RICO
PR

RHODE ISLAND
RI

SOUTH CAROLINA
SC

SOUTH DAKOTA
SD

TENNESSEE
TN

TEXAS
TX

UTAH
UT

VERMONT
VT

VIRGIN ISLANDS
VI

VIRGINIA
VA

WASHINGTON
WA

WEST VIRGINIA
WV

WISCONSIN
WI

WYOMING
WY

Military "State"
Abbreviation

Armed Forces Africa
AE

Armed Forces Americas
(except Canada)
AA

Armed Forces Canada
AE

Armed Forces Europe
AE

Armed Forces Middle East
AE

Armed Forces Pacific
AP

**tsspar** · July 19, 2006, 11:58 AM

Re: Rudimentary Gene Sequencing Question(s)

I live in Minnisota MN is for that ME is standard post office abbrevb. for Maine.