Supplementary Table 1. Loci that MGIP can analyze by default.

Locus Namea Descriptionb Length (nts)c

Standard MLST loci

abcZ putative ABC transporter 433

adk_ adenylate kinase 465

aroE shikimate dehydrogenase 490

fumC fumarate hydratase 465

gdh_ glucose-6-phosphate dehydrogenase

501

pdhC pyruvate dehydrogenase subunit 480

pgm_ phosphoglucomutase 450

Additional MGIP-specific loci

fhb_ factor-H binding protein *

gna2132 unknown *

nadA putative oligomeric coiled-coil adhesin

*

opa opacity porin protein *

porA porin *

porB porin *

fetA iron-regulated outer membrane protein

*

penA penicillin-binding protein 402

a Loci are given by their gene names.b Names/descriptions of the encoded proteins.c Fixed allele sequence lengths are shown; variable lengths are indicated by an asterisk (*).

A

C

B

Supplementary Figure 1. The Strain Table. The strain table shows the MLST profile for each strain or isolate that has been analyzed by an individual user. (A) The strain table loads quickly because ST possibilities are not shown until the user makes a request by clicking on the "View ST Possibilities" link. (B) When there are multiple possibilities, all are shown in a drop down menu. When one of the possibilities is chosen, another request is made to the server to retrieve the ST and its allele components. Alternatively, an icon above the table allows the user to load every strain's ST possibilities at once. (C) One last notable item about the strain table is that it indicates novel STs when it encounters them (e.g. strain 15508).

Supplementary Table 2. Upload speeds for a set of trace files. The average size of a set of trace files in our tests was 11 megabytes (MB). These times do not include processing time.

Size (KB) Speed (KB/second) Label Time (seconds)

11,000 106 Internal Network 0.011

11,000 104 T1 1.1

11,000 2000 FIOS 5.5

11,000 600 Cable 18.3

11,000 400 DSL 27.5

11,000 33 Dial-up 333