SlideShare a Scribd company logo
1 of 1
ArthropodEST: K-State Bioinformatics EST analysis pipeline * Sanjay Chellapilla 1 , Yoonseong Park 2 , Doina Caragea 3  and Susan J. Brown 1 1 Bioinformatics Center, Division of Biology  2 Department of Entomology   3 Department of Computing and Information Sciences Kansas State University, Manhattan KS 66506 ABSTRACT Expressed Sequence Tags (ESTs), produced by single-pass end-sequencing of cDNA clones, generate large datasets that are instrumental in gene discovery and gene sequence determination. Although several EST data analysis pipelines are available on the WWW ( e.g.  ESTpass, EGassembler, ESTexplorer etc.), the WWW-accessible K-State Bioinformatics EST analysis pipeline  ‘ArthropodEST’  goes further than these existing pipelines in providing more options and analyses, along with a user-friendly interface. The pipeline was developed utilizing freely available bioinformatics and system software (academic or F/OSS licenses). Available options in the pipeline include input sequence cleaning and screening for vectors and contaminants, masking repetitive sequences using repeat databases, clustering and assembly into contigs, computing ORFs (Open Reading Frames) and/or signal-peptide predictions, and assigning functional annotations to the contigs and singletons. The pipeline sends out automatic result notification email(s) containing a unique URL to download results from, to the user‘s email address.  A summary report (automatically generated) of the analyses is included in the results available for download. The pipeline is accessible at  http://bioinformatics.ksu.edu/ArthropodEST/ Acknowledgements:   Supported by KSU-TE-AGC (SC), KSU Bioinformatics Center (DC, SC) and K-INBRE (DC, SC). KANSAS STATE UNIVERSITY   KSU BIOINFORMATICS CENTER KSU ARTHROPOD GENOMICS CENTER  K-INBRE Input sequences cleaning Vector/contaminant screening Assembly with optional prior clustering into contigs, singletons User downloads results and report from unique URL automatically sent by email Process user inputs, display project-receipt confirmation and summary, send automatic confirmation email, invoke pipeline shell script Further analyses: functional annotations and/or signal-peptide predictions server-side CGI script server-side Pipeline shell-script client-side (User) client-side (User) ArthropodEST homepage COMPONENTS OF THE PIPELINE (a) System software: GNU/Linux Ubuntu 2.6.24-23-server, bash  3.2.39, Apache 2.2.8 with mod_perl/2.0.3, PERL 5.8.8 with PERL modules CGI 3.29, Mail:Mailer 1.74, File::Temp 0.18, MySQL 5.0 and Postfix 2.5.4 Mail Transport Agent (MTA). (b) Bioinformatics software: - TGICL software suite [ http://compbio.dfci.harvard.edu/tgi/software/ ] -   Vector databases: NCBI UniVec [ http://www.ncbi.nlm.nih.gov/VecScreen/UniVec.html ] EMBL EmVec [ ftp://ftp.ebi.ac.uk/pub/databases/emvec/ ] -   RepeatMasker [ http://www.RepeatMasker.org/ ]  and associated RepBase libraries [ http://www.girinst.org/ ] requires either  cross_match  [ http://www.phrap.org/phredphrapconsed.html ]   or  wu-blastall  [ http://blast.wustl.edu/ ] - CAP3 sequence-assembly program [ http://seq.cs.iastate.edu/ ]     - NCBI BLAST suite [ http://www.ncbi.nlm.nih.gov/BLAST/download.shtml ]   and/or  wu-blastall  [ http://blast.wustl.edu/ ] - blast2GO pipeline version B2G4PIPE [ http://blast2go.bioinfo.cipf.es/ ] -   signalp   [ http://www.cbs.dtu.dk/services/SignalP/ ] and EMBOSS [ http://emboss.sourceforge.net/ ] (c) In-house developed software: WWW-interface HTML/CSS, server-side CGI, PERL, bash shell and awk scripts User-input: project name, e-mail address, input files  and options/parameters for analyses Repeat-masking with standard RepBase libraries WORKFLOW

More Related Content

Similar to Arthropod es tpipeline_poster

Accelerating GWAS epistatic interaction analysis methods
Accelerating GWAS epistatic interaction analysis methodsAccelerating GWAS epistatic interaction analysis methods
Accelerating GWAS epistatic interaction analysis methodsPriscill Orue Esquivel
 
2014 Taverna Tutorial Introduction to eScience and workflows
2014 Taverna Tutorial Introduction to eScience and workflows2014 Taverna Tutorial Introduction to eScience and workflows
2014 Taverna Tutorial Introduction to eScience and workflowsmyGrid team
 
Open Source Software Tools for Synchrophasor Applications
Open Source Software Tools for  Synchrophasor ApplicationsOpen Source Software Tools for  Synchrophasor Applications
Open Source Software Tools for Synchrophasor ApplicationsLuigi Vanfretti
 
How can you access PubChem programmatically?
How can you access PubChem programmatically?How can you access PubChem programmatically?
How can you access PubChem programmatically?Sunghwan Kim
 
Imgc2011 bioinformatics tutorial
Imgc2011 bioinformatics tutorialImgc2011 bioinformatics tutorial
Imgc2011 bioinformatics tutorialDeanna Church
 
How to be a bioinformatician
How to be a bioinformaticianHow to be a bioinformatician
How to be a bioinformaticianChristian Frech
 
CromoCat: New developpments to genetic diversity databasing
CromoCat: New developpments to genetic diversity databasingCromoCat: New developpments to genetic diversity databasing
CromoCat: New developpments to genetic diversity databasingssuser90148d
 
1st KeyStone Summer School - Hackathon Challenge
1st KeyStone Summer School - Hackathon Challenge1st KeyStone Summer School - Hackathon Challenge
1st KeyStone Summer School - Hackathon ChallengeJoel Azzopardi
 
Jeff Grethe: CAMERA
Jeff Grethe: CAMERAJeff Grethe: CAMERA
Jeff Grethe: CAMERAIddo
 
Datasets and tools_from_ncbi_and_elsewhere_for_microbiome_research_v_62817
Datasets and tools_from_ncbi_and_elsewhere_for_microbiome_research_v_62817Datasets and tools_from_ncbi_and_elsewhere_for_microbiome_research_v_62817
Datasets and tools_from_ncbi_and_elsewhere_for_microbiome_research_v_62817Ben Busby
 
Una estrategia para la integración de ontologías, servicios web y PLN en el a...
Una estrategia para la integración de ontologías, servicios web y PLN en el a...Una estrategia para la integración de ontologías, servicios web y PLN en el a...
Una estrategia para la integración de ontologías, servicios web y PLN en el a...Anubis Hosein
 
Galaxy dna-seq-variant calling-presentationandpractical_gent_april-2016
Galaxy dna-seq-variant calling-presentationandpractical_gent_april-2016Galaxy dna-seq-variant calling-presentationandpractical_gent_april-2016
Galaxy dna-seq-variant calling-presentationandpractical_gent_april-2016Prof. Wim Van Criekinge
 
Making Use of NGS Data: From Reads to Trees and Annotations
Making Use of NGS Data: From Reads to Trees and AnnotationsMaking Use of NGS Data: From Reads to Trees and Annotations
Making Use of NGS Data: From Reads to Trees and AnnotationsJoão André Carriço
 

Similar to Arthropod es tpipeline_poster (20)

Accelerating GWAS epistatic interaction analysis methods
Accelerating GWAS epistatic interaction analysis methodsAccelerating GWAS epistatic interaction analysis methods
Accelerating GWAS epistatic interaction analysis methods
 
Understanding Genome
Understanding Genome Understanding Genome
Understanding Genome
 
2014 Taverna Tutorial Introduction to eScience and workflows
2014 Taverna Tutorial Introduction to eScience and workflows2014 Taverna Tutorial Introduction to eScience and workflows
2014 Taverna Tutorial Introduction to eScience and workflows
 
biorepository
biorepositorybiorepository
biorepository
 
Open Source Software Tools for Synchrophasor Applications
Open Source Software Tools for  Synchrophasor ApplicationsOpen Source Software Tools for  Synchrophasor Applications
Open Source Software Tools for Synchrophasor Applications
 
D1803012022
D1803012022D1803012022
D1803012022
 
How can you access PubChem programmatically?
How can you access PubChem programmatically?How can you access PubChem programmatically?
How can you access PubChem programmatically?
 
Imgc2011 bioinformatics tutorial
Imgc2011 bioinformatics tutorialImgc2011 bioinformatics tutorial
Imgc2011 bioinformatics tutorial
 
How to be a bioinformatician
How to be a bioinformaticianHow to be a bioinformatician
How to be a bioinformatician
 
Full Resume
Full ResumeFull Resume
Full Resume
 
EMBL- European Molecular Biology Laboratory
EMBL- European Molecular Biology LaboratoryEMBL- European Molecular Biology Laboratory
EMBL- European Molecular Biology Laboratory
 
Genome comparision
Genome comparisionGenome comparision
Genome comparision
 
CromoCat: New developpments to genetic diversity databasing
CromoCat: New developpments to genetic diversity databasingCromoCat: New developpments to genetic diversity databasing
CromoCat: New developpments to genetic diversity databasing
 
1st KeyStone Summer School - Hackathon Challenge
1st KeyStone Summer School - Hackathon Challenge1st KeyStone Summer School - Hackathon Challenge
1st KeyStone Summer School - Hackathon Challenge
 
Jeff Grethe: CAMERA
Jeff Grethe: CAMERAJeff Grethe: CAMERA
Jeff Grethe: CAMERA
 
cpc-152-2-2003
cpc-152-2-2003cpc-152-2-2003
cpc-152-2-2003
 
Datasets and tools_from_ncbi_and_elsewhere_for_microbiome_research_v_62817
Datasets and tools_from_ncbi_and_elsewhere_for_microbiome_research_v_62817Datasets and tools_from_ncbi_and_elsewhere_for_microbiome_research_v_62817
Datasets and tools_from_ncbi_and_elsewhere_for_microbiome_research_v_62817
 
Una estrategia para la integración de ontologías, servicios web y PLN en el a...
Una estrategia para la integración de ontologías, servicios web y PLN en el a...Una estrategia para la integración de ontologías, servicios web y PLN en el a...
Una estrategia para la integración de ontologías, servicios web y PLN en el a...
 
Galaxy dna-seq-variant calling-presentationandpractical_gent_april-2016
Galaxy dna-seq-variant calling-presentationandpractical_gent_april-2016Galaxy dna-seq-variant calling-presentationandpractical_gent_april-2016
Galaxy dna-seq-variant calling-presentationandpractical_gent_april-2016
 
Making Use of NGS Data: From Reads to Trees and Annotations
Making Use of NGS Data: From Reads to Trees and AnnotationsMaking Use of NGS Data: From Reads to Trees and Annotations
Making Use of NGS Data: From Reads to Trees and Annotations
 

More from Tamizhmuhil

Ayeesha tamil story by Era.Natarajan
Ayeesha tamil story by Era.NatarajanAyeesha tamil story by Era.Natarajan
Ayeesha tamil story by Era.NatarajanTamizhmuhil
 
Ayeesha by Era.Natarajan
Ayeesha by Era.NatarajanAyeesha by Era.Natarajan
Ayeesha by Era.NatarajanTamizhmuhil
 
Tn min-ithazh-pankuni-nanthana
Tn min-ithazh-pankuni-nanthanaTn min-ithazh-pankuni-nanthana
Tn min-ithazh-pankuni-nanthanaTamizhmuhil
 
Algebra formulae
Algebra formulaeAlgebra formulae
Algebra formulaeTamizhmuhil
 
Tn min-ithazh-thai-nanthana
Tn min-ithazh-thai-nanthanaTn min-ithazh-thai-nanthana
Tn min-ithazh-thai-nanthanaTamizhmuhil
 
இந்த வாரம் கலாரசிகன் Dinamani - tamil daily news
இந்த வாரம் கலாரசிகன்   Dinamani - tamil daily newsஇந்த வாரம் கலாரசிகன்   Dinamani - tamil daily news
இந்த வாரம் கலாரசிகன் Dinamani - tamil daily newsTamizhmuhil
 
Kavi visai e-book realesed by tamilaka kavinjar kalai ilakkiya sangam
Kavi visai   e-book realesed by tamilaka kavinjar kalai ilakkiya sangamKavi visai   e-book realesed by tamilaka kavinjar kalai ilakkiya sangam
Kavi visai e-book realesed by tamilaka kavinjar kalai ilakkiya sangamTamizhmuhil
 
Birdhouse gift basket
Birdhouse gift basketBirdhouse gift basket
Birdhouse gift basketTamizhmuhil
 
Cursors in oracle
Cursors in oracleCursors in oracle
Cursors in oracleTamizhmuhil
 

More from Tamizhmuhil (12)

Ayeesha tamil story by Era.Natarajan
Ayeesha tamil story by Era.NatarajanAyeesha tamil story by Era.Natarajan
Ayeesha tamil story by Era.Natarajan
 
Ayeesha by Era.Natarajan
Ayeesha by Era.NatarajanAyeesha by Era.Natarajan
Ayeesha by Era.Natarajan
 
Lecture 343
Lecture 343Lecture 343
Lecture 343
 
Lecture 839
Lecture 839Lecture 839
Lecture 839
 
Tn min-ithazh-pankuni-nanthana
Tn min-ithazh-pankuni-nanthanaTn min-ithazh-pankuni-nanthana
Tn min-ithazh-pankuni-nanthana
 
Kaatruveli
KaatruveliKaatruveli
Kaatruveli
 
Algebra formulae
Algebra formulaeAlgebra formulae
Algebra formulae
 
Tn min-ithazh-thai-nanthana
Tn min-ithazh-thai-nanthanaTn min-ithazh-thai-nanthana
Tn min-ithazh-thai-nanthana
 
இந்த வாரம் கலாரசிகன் Dinamani - tamil daily news
இந்த வாரம் கலாரசிகன்   Dinamani - tamil daily newsஇந்த வாரம் கலாரசிகன்   Dinamani - tamil daily news
இந்த வாரம் கலாரசிகன் Dinamani - tamil daily news
 
Kavi visai e-book realesed by tamilaka kavinjar kalai ilakkiya sangam
Kavi visai   e-book realesed by tamilaka kavinjar kalai ilakkiya sangamKavi visai   e-book realesed by tamilaka kavinjar kalai ilakkiya sangam
Kavi visai e-book realesed by tamilaka kavinjar kalai ilakkiya sangam
 
Birdhouse gift basket
Birdhouse gift basketBirdhouse gift basket
Birdhouse gift basket
 
Cursors in oracle
Cursors in oracleCursors in oracle
Cursors in oracle
 

Recently uploaded

HED Office Sohayok Exam Question Solution 2023.pdf
HED Office Sohayok Exam Question Solution 2023.pdfHED Office Sohayok Exam Question Solution 2023.pdf
HED Office Sohayok Exam Question Solution 2023.pdfMohonDas
 
Ultra structure and life cycle of Plasmodium.pptx
Ultra structure and life cycle of Plasmodium.pptxUltra structure and life cycle of Plasmodium.pptx
Ultra structure and life cycle of Plasmodium.pptxDr. Asif Anas
 
Human-AI Co-Creation of Worked Examples for Programming Classes
Human-AI Co-Creation of Worked Examples for Programming ClassesHuman-AI Co-Creation of Worked Examples for Programming Classes
Human-AI Co-Creation of Worked Examples for Programming ClassesMohammad Hassany
 
In - Vivo and In - Vitro Correlation.pptx
In - Vivo and In - Vitro Correlation.pptxIn - Vivo and In - Vitro Correlation.pptx
In - Vivo and In - Vitro Correlation.pptxAditiChauhan701637
 
How to Add a many2many Relational Field in Odoo 17
How to Add a many2many Relational Field in Odoo 17How to Add a many2many Relational Field in Odoo 17
How to Add a many2many Relational Field in Odoo 17Celine George
 
Patient Counselling. Definition of patient counseling; steps involved in pati...
Patient Counselling. Definition of patient counseling; steps involved in pati...Patient Counselling. Definition of patient counseling; steps involved in pati...
Patient Counselling. Definition of patient counseling; steps involved in pati...raviapr7
 
Prescribed medication order and communication skills.pptx
Prescribed medication order and communication skills.pptxPrescribed medication order and communication skills.pptx
Prescribed medication order and communication skills.pptxraviapr7
 
Education and training program in the hospital APR.pptx
Education and training program in the hospital APR.pptxEducation and training program in the hospital APR.pptx
Education and training program in the hospital APR.pptxraviapr7
 
P4C x ELT = P4ELT: Its Theoretical Background (Kanazawa, 2024 March).pdf
P4C x ELT = P4ELT: Its Theoretical Background (Kanazawa, 2024 March).pdfP4C x ELT = P4ELT: Its Theoretical Background (Kanazawa, 2024 March).pdf
P4C x ELT = P4ELT: Its Theoretical Background (Kanazawa, 2024 March).pdfYu Kanazawa / Osaka University
 
How to Add Existing Field in One2Many Tree View in Odoo 17
How to Add Existing Field in One2Many Tree View in Odoo 17How to Add Existing Field in One2Many Tree View in Odoo 17
How to Add Existing Field in One2Many Tree View in Odoo 17Celine George
 
Patterns of Written Texts Across Disciplines.pptx
Patterns of Written Texts Across Disciplines.pptxPatterns of Written Texts Across Disciplines.pptx
Patterns of Written Texts Across Disciplines.pptxMYDA ANGELICA SUAN
 
DUST OF SNOW_BY ROBERT FROST_EDITED BY_ TANMOY MISHRA
DUST OF SNOW_BY ROBERT FROST_EDITED BY_ TANMOY MISHRADUST OF SNOW_BY ROBERT FROST_EDITED BY_ TANMOY MISHRA
DUST OF SNOW_BY ROBERT FROST_EDITED BY_ TANMOY MISHRATanmoy Mishra
 
Clinical Pharmacy Introduction to Clinical Pharmacy, Concept of clinical pptx
Clinical Pharmacy  Introduction to Clinical Pharmacy, Concept of clinical pptxClinical Pharmacy  Introduction to Clinical Pharmacy, Concept of clinical pptx
Clinical Pharmacy Introduction to Clinical Pharmacy, Concept of clinical pptxraviapr7
 
How to Use api.constrains ( ) in Odoo 17
How to Use api.constrains ( ) in Odoo 17How to Use api.constrains ( ) in Odoo 17
How to Use api.constrains ( ) in Odoo 17Celine George
 
3.21.24 The Origins of Black Power.pptx
3.21.24  The Origins of Black Power.pptx3.21.24  The Origins of Black Power.pptx
3.21.24 The Origins of Black Power.pptxmary850239
 
5 charts on South Africa as a source country for international student recrui...
5 charts on South Africa as a source country for international student recrui...5 charts on South Africa as a source country for international student recrui...
5 charts on South Africa as a source country for international student recrui...CaraSkikne1
 
What is the Future of QuickBooks DeskTop?
What is the Future of QuickBooks DeskTop?What is the Future of QuickBooks DeskTop?
What is the Future of QuickBooks DeskTop?TechSoup
 
PISA-VET launch_El Iza Mohamedou_19 March 2024.pptx
PISA-VET launch_El Iza Mohamedou_19 March 2024.pptxPISA-VET launch_El Iza Mohamedou_19 March 2024.pptx
PISA-VET launch_El Iza Mohamedou_19 March 2024.pptxEduSkills OECD
 

Recently uploaded (20)

HED Office Sohayok Exam Question Solution 2023.pdf
HED Office Sohayok Exam Question Solution 2023.pdfHED Office Sohayok Exam Question Solution 2023.pdf
HED Office Sohayok Exam Question Solution 2023.pdf
 
Ultra structure and life cycle of Plasmodium.pptx
Ultra structure and life cycle of Plasmodium.pptxUltra structure and life cycle of Plasmodium.pptx
Ultra structure and life cycle of Plasmodium.pptx
 
Human-AI Co-Creation of Worked Examples for Programming Classes
Human-AI Co-Creation of Worked Examples for Programming ClassesHuman-AI Co-Creation of Worked Examples for Programming Classes
Human-AI Co-Creation of Worked Examples for Programming Classes
 
In - Vivo and In - Vitro Correlation.pptx
In - Vivo and In - Vitro Correlation.pptxIn - Vivo and In - Vitro Correlation.pptx
In - Vivo and In - Vitro Correlation.pptx
 
How to Add a many2many Relational Field in Odoo 17
How to Add a many2many Relational Field in Odoo 17How to Add a many2many Relational Field in Odoo 17
How to Add a many2many Relational Field in Odoo 17
 
Patient Counselling. Definition of patient counseling; steps involved in pati...
Patient Counselling. Definition of patient counseling; steps involved in pati...Patient Counselling. Definition of patient counseling; steps involved in pati...
Patient Counselling. Definition of patient counseling; steps involved in pati...
 
Prescribed medication order and communication skills.pptx
Prescribed medication order and communication skills.pptxPrescribed medication order and communication skills.pptx
Prescribed medication order and communication skills.pptx
 
Education and training program in the hospital APR.pptx
Education and training program in the hospital APR.pptxEducation and training program in the hospital APR.pptx
Education and training program in the hospital APR.pptx
 
P4C x ELT = P4ELT: Its Theoretical Background (Kanazawa, 2024 March).pdf
P4C x ELT = P4ELT: Its Theoretical Background (Kanazawa, 2024 March).pdfP4C x ELT = P4ELT: Its Theoretical Background (Kanazawa, 2024 March).pdf
P4C x ELT = P4ELT: Its Theoretical Background (Kanazawa, 2024 March).pdf
 
How to Add Existing Field in One2Many Tree View in Odoo 17
How to Add Existing Field in One2Many Tree View in Odoo 17How to Add Existing Field in One2Many Tree View in Odoo 17
How to Add Existing Field in One2Many Tree View in Odoo 17
 
Patterns of Written Texts Across Disciplines.pptx
Patterns of Written Texts Across Disciplines.pptxPatterns of Written Texts Across Disciplines.pptx
Patterns of Written Texts Across Disciplines.pptx
 
DUST OF SNOW_BY ROBERT FROST_EDITED BY_ TANMOY MISHRA
DUST OF SNOW_BY ROBERT FROST_EDITED BY_ TANMOY MISHRADUST OF SNOW_BY ROBERT FROST_EDITED BY_ TANMOY MISHRA
DUST OF SNOW_BY ROBERT FROST_EDITED BY_ TANMOY MISHRA
 
Clinical Pharmacy Introduction to Clinical Pharmacy, Concept of clinical pptx
Clinical Pharmacy  Introduction to Clinical Pharmacy, Concept of clinical pptxClinical Pharmacy  Introduction to Clinical Pharmacy, Concept of clinical pptx
Clinical Pharmacy Introduction to Clinical Pharmacy, Concept of clinical pptx
 
Personal Resilience in Project Management 2 - TV Edit 1a.pdf
Personal Resilience in Project Management 2 - TV Edit 1a.pdfPersonal Resilience in Project Management 2 - TV Edit 1a.pdf
Personal Resilience in Project Management 2 - TV Edit 1a.pdf
 
Finals of Kant get Marx 2.0 : a general politics quiz
Finals of Kant get Marx 2.0 : a general politics quizFinals of Kant get Marx 2.0 : a general politics quiz
Finals of Kant get Marx 2.0 : a general politics quiz
 
How to Use api.constrains ( ) in Odoo 17
How to Use api.constrains ( ) in Odoo 17How to Use api.constrains ( ) in Odoo 17
How to Use api.constrains ( ) in Odoo 17
 
3.21.24 The Origins of Black Power.pptx
3.21.24  The Origins of Black Power.pptx3.21.24  The Origins of Black Power.pptx
3.21.24 The Origins of Black Power.pptx
 
5 charts on South Africa as a source country for international student recrui...
5 charts on South Africa as a source country for international student recrui...5 charts on South Africa as a source country for international student recrui...
5 charts on South Africa as a source country for international student recrui...
 
What is the Future of QuickBooks DeskTop?
What is the Future of QuickBooks DeskTop?What is the Future of QuickBooks DeskTop?
What is the Future of QuickBooks DeskTop?
 
PISA-VET launch_El Iza Mohamedou_19 March 2024.pptx
PISA-VET launch_El Iza Mohamedou_19 March 2024.pptxPISA-VET launch_El Iza Mohamedou_19 March 2024.pptx
PISA-VET launch_El Iza Mohamedou_19 March 2024.pptx
 

Arthropod es tpipeline_poster

  • 1. ArthropodEST: K-State Bioinformatics EST analysis pipeline * Sanjay Chellapilla 1 , Yoonseong Park 2 , Doina Caragea 3 and Susan J. Brown 1 1 Bioinformatics Center, Division of Biology 2 Department of Entomology 3 Department of Computing and Information Sciences Kansas State University, Manhattan KS 66506 ABSTRACT Expressed Sequence Tags (ESTs), produced by single-pass end-sequencing of cDNA clones, generate large datasets that are instrumental in gene discovery and gene sequence determination. Although several EST data analysis pipelines are available on the WWW ( e.g. ESTpass, EGassembler, ESTexplorer etc.), the WWW-accessible K-State Bioinformatics EST analysis pipeline ‘ArthropodEST’ goes further than these existing pipelines in providing more options and analyses, along with a user-friendly interface. The pipeline was developed utilizing freely available bioinformatics and system software (academic or F/OSS licenses). Available options in the pipeline include input sequence cleaning and screening for vectors and contaminants, masking repetitive sequences using repeat databases, clustering and assembly into contigs, computing ORFs (Open Reading Frames) and/or signal-peptide predictions, and assigning functional annotations to the contigs and singletons. The pipeline sends out automatic result notification email(s) containing a unique URL to download results from, to the user‘s email address. A summary report (automatically generated) of the analyses is included in the results available for download. The pipeline is accessible at http://bioinformatics.ksu.edu/ArthropodEST/ Acknowledgements: Supported by KSU-TE-AGC (SC), KSU Bioinformatics Center (DC, SC) and K-INBRE (DC, SC). KANSAS STATE UNIVERSITY KSU BIOINFORMATICS CENTER KSU ARTHROPOD GENOMICS CENTER K-INBRE Input sequences cleaning Vector/contaminant screening Assembly with optional prior clustering into contigs, singletons User downloads results and report from unique URL automatically sent by email Process user inputs, display project-receipt confirmation and summary, send automatic confirmation email, invoke pipeline shell script Further analyses: functional annotations and/or signal-peptide predictions server-side CGI script server-side Pipeline shell-script client-side (User) client-side (User) ArthropodEST homepage COMPONENTS OF THE PIPELINE (a) System software: GNU/Linux Ubuntu 2.6.24-23-server, bash 3.2.39, Apache 2.2.8 with mod_perl/2.0.3, PERL 5.8.8 with PERL modules CGI 3.29, Mail:Mailer 1.74, File::Temp 0.18, MySQL 5.0 and Postfix 2.5.4 Mail Transport Agent (MTA). (b) Bioinformatics software: - TGICL software suite [ http://compbio.dfci.harvard.edu/tgi/software/ ] - Vector databases: NCBI UniVec [ http://www.ncbi.nlm.nih.gov/VecScreen/UniVec.html ] EMBL EmVec [ ftp://ftp.ebi.ac.uk/pub/databases/emvec/ ] - RepeatMasker [ http://www.RepeatMasker.org/ ] and associated RepBase libraries [ http://www.girinst.org/ ] requires either cross_match [ http://www.phrap.org/phredphrapconsed.html ] or wu-blastall [ http://blast.wustl.edu/ ] - CAP3 sequence-assembly program [ http://seq.cs.iastate.edu/ ]     - NCBI BLAST suite [ http://www.ncbi.nlm.nih.gov/BLAST/download.shtml ] and/or wu-blastall [ http://blast.wustl.edu/ ] - blast2GO pipeline version B2G4PIPE [ http://blast2go.bioinfo.cipf.es/ ] - signalp [ http://www.cbs.dtu.dk/services/SignalP/ ] and EMBOSS [ http://emboss.sourceforge.net/ ] (c) In-house developed software: WWW-interface HTML/CSS, server-side CGI, PERL, bash shell and awk scripts User-input: project name, e-mail address, input files and options/parameters for analyses Repeat-masking with standard RepBase libraries WORKFLOW