Bioinformatics on-campus services and fees:
Bioinformatics Fees: High Throughput DNA Sequencing Projects
Deluxe Bioinformatics
fees: $0.50/sequence, $48/per 96-well plate; $0.25/sequence, $24/per 96-well
plate after 30,000 sequences in a GPMS (below) project. Data processing expands on basic
bioinformatics (base calling by Phred, electropherogram, success rate estimate
per plate) and includes the following steps and programs: quality check based
on Phred scores using Qualtrim, vector trimming using cross_match, and
screening for E. coli genomic DNA, rRNA, mtDNA, viral DNA or RNA via BLAST.
Data are stored on a server for the duration of the project and can be
downloaded through a password protected website including chromatographs,
untrimmed sequences, cleaned up sequences, and a success rate report. If
Advanced Bioinformatics Service is used, data will be handled by GPMS.
The Genome Project
Management System (GPMS) has been
developed for data management in a high throughput sequencing project. Advanced
bioinformatics tools and services will be provided for a one-time set-up fee of
$10,000. The set-up fee will cover a user account on the GPMS system, technical
support, database maintenance, database updates, storage disk, data backup and
access to all functional modules of the GPMS system. GPMS provides summaries
and statistics of high throughput sequencing projects. Users can monitor
sequencing progress and success rate in detail and real time. Users can also
browse through subprojects, plates, and individual sequences and get first hand
information about their sequences online including electropherogram, identified
repeat regions, the nature of the filtered sequences, etc. Users can also query
and download electropherogram and sequences in fasta format. Other functions of
GPMS include GenBank submission and full access to GridBLAST (see below
"GridBLAST" service).
Sequence Assembly,
Annotation, and Project Databases for
Public Access $10,000
For EST projects, the service includes the following items:
Redundancy checking: Trimmed and filtered sequences will be assembled using Phrap to generate
contigs. The redundancy will be calculated as (1- (C+S)/T) x 100%, where C is
the number of contigs; S is the number of singletons and singlets; T is the
total number of sequences. If requested, we will also compare any newly sequenced
sequences against the previously sequenced sequences using BLASTN to estimated
redundancy.
Clustering and Assembly: Upon request or pre-determined criteria, we will perform EST clustering and
assembly using the Paracel Transcript Assembler (PTA). The clustering and
assembly can be done using only the sequences generated from the project or
combined with any public available sequences.
Annotation: Based on pre-determined criteria, we will provide annotation to the assembled or
unassembled ESTs using BLAST against multiple databases. We will also make
association with Gene Ontology terms as part of the annotation.
Clone picking for microarray or 3' sequencing: In many cases, the purpose of an EST project is to
construct a custom microarray. For EST contigs, we need a strategy or an
algorithm to pick one sequence (or clone) to represent each contig in the
microarray. In another case, if continued sequencing from another end (e.g.
3'end) is desired, we also need a strategy to pick a clone from a contig assembled
from previously sequenced sequences (e.g. 5' end sequences). We will work with
investigators to design and implement the clone picking strategy and provide a
list of clones that best represent the contigs.
Public database: In most of cases, we need to set up an EST project database for public access including
annotations. The Bioinformatics Unit has developed the EST Information and
Annotation Management System (ESTIMA). We will set up a project web site and
use ESTIMA for public access to the annotated EST information. We will keep the
database updated with new annotation and new sequences if more are available.
ESTIMA is web based database system. People can query the EST sequences and their annotations in
many ways including searching by sequence ID or Genbank Accession number,
searching by Gene Ontology terms, searching by keyword in annotation, searching
by contigs, and searching by BLAST. Once the microarray is built, ESTIMA can
also serve as annotation system for the genes on the microarray.
For other sequencing projects (e.g. microbial genomes, BAC ends, BAC shotgun or Genome shotgun), the
tasks will be different, but most likely include assembly, annotation, and web
based databases. For these kinds of projects and other analyses such as phylogenetic
analysis, comparative genomics, please consult with, Dr.
Thimmapuram (217.244.7355, jyothit@illinois.edu
), for more information.
To continue the maintenance and update of the databases (including both GPMS and ESTIMA) on our
servers, an annual fee of $2,000 will be charged for each subsequent year. If a
project is not renewed, the user GPMS account will be disabled. The ESTIMA
sites will not be updated. All data will be archived and then removed from the
system. The Bioinformatics Unit will provide a copy of all archived data to the
user.
Microarray Analysis:
Affymetrix GeneChips and Spotted Microarray,
Experiment Design, Statistical Analysis, Data Mining, Annotation, and Databases
The Bioinformatics Unit provides general consulting service for microarray analysis including both Affymetrix GeneChips and Spotted Microarray (cDNA or Oligo array):
Initial consultation: FREE
Includes experimental design, sample size considerations, and general statistical analysis options. It is highly recommended before the experiment is begun.
Basic statistical analysis: $300 and up, depending on number of slides
Quality control assessments, data preprocessing and statistical analysis to generate lists of differentially expressed genes. See the Microarray Analysis and Service page for more details.
Data mining of statistical results: $300 per experiment
In-depth exploration of the lists of differentially expressed genes, including visualizing relationships using GeneSpring and detailed annotation using Gene Set Enrichment Analysis and PathwayAssist. See the Microarray Analysis and Service page [link this to details page] for more details.
Microarray Database and MIAME Compliance: coming soon
When publishing papers with microarray data, most of journals will require public access of microarray data and more and more journal will require data in MIAME compliant format. The Bioinformatics Unit can provide solutions for these requirements through a local microarray database or submission to a public repository. A separate fee may be established depending on the scope of the work.
General consulting services: $50 per hour
High Performance Computing,
The Bioinformatics Unit
maintains several large server computers and many software programs that are used
for biological research. We have opened the largest server, which has 32
processors and 16 G shared memory, to campus for research computing related to
biological studies. There are two services available:
We have developed a BLAST portal for running large BLAST jobs. The
portal is a wrapper for SGI HT-BLAST. Through the portal, a user can upload
query files then run BLAST programs including BLASTN, BLASTX, BLASTP, TBLASTN,
and TBLASTX or Formatdb to make the uploaded query file searchable by BLAST.
After a job submission, the user will receive an e-mail notification when the
job starts executing. A user can see the job status (queued, running, finished,
aborted) online. After the job is finished, the user will receive an e-mail
notification. He/She then can parse, download, and query the results in the
GridBLAST portal. We maintain and update the public databases for BLAST, mainly
from NCBI. We can also maintain any additional databases upon request. To use
the service, a user need to register an account for the portal and can work
from any computer with a web browser. We recommend using Internet Explore 5.0
or higher version. Fees cover disk space and account maintenance.
Oligonucleotide design for microarrays, for GPMS users a $1000 set up charge, plus $0.30 per oligonucleotide.
General computing account is $500/year per account is
a Unix account on the server can be requested for computing OTHER THAN BLAST.
With this account, a user can access most of the licensed software and freeware
programs on the server as listed below:
. Statistics Packages: SAS, R, Matlab
. Bioinformatics Packages: EMBOSS, Staten
. Genome Sequence related: Phred/Phrap/Cross_match, CAP3, RepeatMasker
In addition to the services listed above, the
Bioinformatics Unit also provide consulting (at $50 per hour) on many other
aspects in bioinformatics, which include but not limited to the following:
. Database and data warehouse design and development
. Web based database system development
. Automation of data processing and pipeline
. Network/pathway analysis
. Pattern/motif search and promoter analysis
Bioinformatics for Genome Sequencer FLX Titanium
Users get a quality trimmed FASTA file (sequence and quality scores) when no other bioinformatics services are requested.
The following prices are only for guidance and vary with the requirements of the projects.
Microbial Genome Assembly (w/o gap closure) and Annotation: Up to 1 million reads
- Assembly using Newbler: $500 (per assembly)
- Annotation – local MANATEE database setup and nr BLAST annotation: $2500 per assembly
- Maintenance: $300 per year (per genome, after first year).
- Assembly and mapping to a reference genome: $1000 (per analysis)
- Please contact us if you have more than one bulk plate
cDNA library: Up to 1 million Titanium reads
- Trimming adaptors: $500 per project
- Assembly - if only FLX-Titanium data: $1000 (per assembly)
- Assembly combining FLX-Titanium and Sanger data (up to 20K sequences): $1500 (per assembly)
- Annotation: $2,500
- Please contact us if you have more than one bulk plate per genome
Genomic library: Assembly (w/o gap closure) and Annotation: Up to 1 million Titanium reads
- Assembly using Newbler - if only FLX- Titanium data: $500 (per assembly)
- Assembly combining FLX- Titanium and Sanger data (up to 20K sequences): $1000 (per assembly)
- Annotation: $3,000
- Please contact us if you have more than one bulk plate per genome
Amplicon analysis: Up to 1 million reads
- Sorting reads by MIDs: $500 per bulk plate (up to 1 million reads).
- Sorting reads based on MIDs, trimming gene-specific primers and low quality bases and sorting based on length: $1000 per project.
(all sff files will be combined before processing)
- Analysis by DOTUR, MEGAN, FastGroup – contact us details.
Assembly and Annotation of larger genomes: fee may vary based on the size of the project – please contact us for details
SNP mining – contact us for details
Bioinformatics for Genome Analyzer II (Solexa/Illumina)
Users get sequence and quality scores in fastq format when no other bioinformatics services are requested.
Primary analysis - Alignment to reference genome:
$1000 per lane aligned to one genome or a set of genes
(subsequent lanes $500/lane if the same genome is used)
Please note that s_N_sequence.txt and s_N_sorted.txt files will be provided.
Secondary analysis:
This varies with the project. Please contact us for details
***This is an abridged list of our service prices and subject to change at any time; please contact Dr. Jyothi Thimmapuram of Bioinformatics, at (217) 265-5061 or jyothit@illinois.edu for information on prices and other issues related to your project.***
Fees for facility users from universities other than the University of Illinois or other State of Illinois Universities are 25.3% above on-campus rates., For projects from off-campus users exceeding $5,000 a contract must be negotiated through the Grants & Contracts Office of the University of Illinois. Contact Dr. Mark A. Mikel (217.244.0144, mmikel@illinois.edu), Associate Director of the Roy J. Carver Biotechnology Center, to for further information.
*All services are provided on a best effort basis and must be paid, failure or success unless stated otherwise*
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