LASSAP, a LArge Scale Sequence compArison Package
Motivation: This paper presents LASSAP, a new software package for sequence comparison. LASSAP is a programmable, high-performance system designed to raise current limitations of sequence comparison programs in order to fit the needs of large-scale analysis. LASSAP provides an API (Application Progr...
Uloženo v:
| Vydáno v: | Bioinformatics Ročník 13; číslo 2; s. 137 - 143 |
|---|---|
| Hlavní autoři: | , |
| Médium: | Journal Article |
| Jazyk: | angličtina |
| Vydáno: |
Washington, DC
Oxford University Press
01.04.1997
Oxford |
| Témata: | |
| ISSN: | 0266-7061, 1367-4803, 1460-2059 |
| On-line přístup: | Získat plný text |
| Tagy: |
Přidat tag
Žádné tagy, Buďte první, kdo vytvoří štítek k tomuto záznamu!
|
| Abstract | Motivation: This paper presents LASSAP, a new software package for sequence comparison. LASSAP is a programmable, high-performance system designed to raise current limitations of sequence comparison programs in order to fit the needs of large-scale analysis. LASSAP provides an API (Application Programming Interface) allowing the integration of any generic pairwise-based algorithm. Results: Whatever pairwise algorithm is used in LASSAP, it shares with all other algorithms numerous enhancements such as: (i) intra- and inter-databank comparisons; (ii) computational requests (selections and computations are achieved on the fly); (iii) frame translations on queries and databanks; (iv) structured results allowing easy and powerful post-analysis; (v) performance improvements by parallelization and the driving of specialized hardware. LASSAP currently implements all major sequence comparison algorithms (Fasta, Blast, Smith/Waterman), and other string matching and pattern matching algorithms. LASSAP is both an integrated software for end-users and a framework allowing the integration and the combination of new algorithms. LASSAP is used in different projects such as the building of PRODOM, the exhaustive comparison of yeast sequences, and the subfragments matching problem of TREMBL. |
|---|---|
| AbstractList | This paper presents LASSAP, a new software package for sequence comparison. LASSAP is a programmable, high-performance system designed to raise current limitations of sequence comparison programs in order to fit the needs of large-scale analysis. LASSAP provides an API (Application Programming Interface) allowing the integration of any generic pairwise-based algorithm.
Whatever pairwise algorithm is used in LASSAP, it shares with all other algorithms numerous enhancements such as: (i) intra- and inter-databank comparisons; (ii) computational requests (selections and computations are achieved on the fly); (iii) frame translations on queries and databanks; (iv) structured results allowing easy and powerful post-analysis; (v) performance improvements by parallelization and the driving of specialized hardware. LASSAP currently implements all major sequence comparison algorithms (Fasta, Blast, Smith/Waterman), and other string matching and pattern matching algorithms. LASSAP is both an integrated software for end-users and a framework allowing the integration and the combination of new algorithms. LASSAP is used in different projects such as the building of PRODOM, the exhaustive comparison of yeast sequences, and the subfragments matching problem of TREMBL. Motivation: This paper presents LASSAP, a new software package for sequence comparison. LASSAP is a programmable, high-performance system designed to raise current limitations of sequence comparison programs in order to fit the needs of large-scale analysis. LASSAP provides an API (Application Programming Interface) allowing the integration of any generic pairwise-based algorithm. Results: Whatever pairwise algorithm is used in LASSAP, it shares with all other algorithms numerous enhancements such as: (i) intra- and inter-databank comparisons; (ii) computational requests (selections and computations are achieved on the fly); (iii) frame translations on queries and databanks; (iv) structured results allowing easy and powerful post-analysis; (v) performance improvements by parallelization and the driving of specialized hardware. LASSAP currently implements all major sequence comparison algorithms (Fasta, Blast, Smith/Waterman), and other string matching and pattern matching algorithms. LASSAP is both an integrated software for end-users and a framework allowing the integration and the combination of new algorithms. LASSAP is used in different projects such as the building of PRODOM, the exhaustive comparison of yeast sequences, and the subfragments matching problem of TREMBL. Motivation This paper presents LASSAP, a new software package for sequence comparison. LASSAP is a programmable, high-performance system designed to raise current limitations of sequence comparison programs in order to fit the needs of large-scale analysis. LASSAP provides an API (Application Programming Interface) allowing the integration of any generic pairwise-based algorithm. Results Whatever pairwise algorithm is used in LASSAP, it shares with all other algorithms numerous enhancements such as: (i) intra- and inter-databank comparisons; (ii) computational requests (selections and computations are achieved on the fly); (iii) frame translations on queries and databanks; (iv) structured results allowing easy and powerful post-analysis; (v) performance improvements by parallelization and the driving of specialized hardware. LASSAP currently implements all major sequence comparison algorithms (Fasta, Blast, Smith/Waterman), and other string matching and pattern matching algorithms. LASSAP is both an integrated software for end-users and a framework allowing the integration and the combination of new algorithms. LASSAP is used in different projects such as the building of PRODOM, the exhaustive comparison of yeast sequences, and the subfragments matching problem of TREMBL. Availability Binaries for Unix and documentations are available at the following address: http://www-rocq.inria.fr/genome Contact E-mail: Eric.Glemet@inria.fr, Jean-Jacques.Coda-ni@inria.fr This paper presents LASSAP, a new software package for sequence comparison. LASSAP is a programmable, high-performance system designed to raise current limitations of sequence comparison programs in order to fit the needs of large-scale analysis. LASSAP provides an API (Application Programming Interface) allowing the integration of any generic pairwise-based algorithm.MOTIVATIONThis paper presents LASSAP, a new software package for sequence comparison. LASSAP is a programmable, high-performance system designed to raise current limitations of sequence comparison programs in order to fit the needs of large-scale analysis. LASSAP provides an API (Application Programming Interface) allowing the integration of any generic pairwise-based algorithm.Whatever pairwise algorithm is used in LASSAP, it shares with all other algorithms numerous enhancements such as: (i) intra- and inter-databank comparisons; (ii) computational requests (selections and computations are achieved on the fly); (iii) frame translations on queries and databanks; (iv) structured results allowing easy and powerful post-analysis; (v) performance improvements by parallelization and the driving of specialized hardware. LASSAP currently implements all major sequence comparison algorithms (Fasta, Blast, Smith/Waterman), and other string matching and pattern matching algorithms. LASSAP is both an integrated software for end-users and a framework allowing the integration and the combination of new algorithms. LASSAP is used in different projects such as the building of PRODOM, the exhaustive comparison of yeast sequences, and the subfragments matching problem of TREMBL.RESULTSWhatever pairwise algorithm is used in LASSAP, it shares with all other algorithms numerous enhancements such as: (i) intra- and inter-databank comparisons; (ii) computational requests (selections and computations are achieved on the fly); (iii) frame translations on queries and databanks; (iv) structured results allowing easy and powerful post-analysis; (v) performance improvements by parallelization and the driving of specialized hardware. LASSAP currently implements all major sequence comparison algorithms (Fasta, Blast, Smith/Waterman), and other string matching and pattern matching algorithms. LASSAP is both an integrated software for end-users and a framework allowing the integration and the combination of new algorithms. LASSAP is used in different projects such as the building of PRODOM, the exhaustive comparison of yeast sequences, and the subfragments matching problem of TREMBL. |
| Author | Codani, J.J Glemet, E |
| Author_xml | – sequence: 1 fullname: Glemet, E – sequence: 2 fullname: Codani, J.J |
| BackLink | http://pascal-francis.inist.fr/vibad/index.php?action=getRecordDetail&idt=2632403$$DView record in Pascal Francis https://www.ncbi.nlm.nih.gov/pubmed/9146960$$D View this record in MEDLINE/PubMed |
| BookMark | eNqFkcFq3DAQhkVJSTdpH6HEh9JTvNFYsmQdenBCkxQMDWwTSi5iLMuLGtvaSF5o3z4Kuw20l8Awc5jvn5HmPyIHk58sISdAl0AVO2udd1Pvw4izM_EM2LJYApNvyAK4oHlBS3VAFrQQIpdUwDtyFOMvSkvgnB-SQ5UoJeiCQFOvVvXNaYZZU4e1zVYGh5Tt49ZOxmbGj5s6uOin7AbNA67te_K2xyHaD_t6TG4vv_64uM6b71ffLuomNxxgzsFa1XbcKqiUUGXXp5AdMiwpM0KwtpKgsIK-r7DDVijaIQorDUewQil2TD7v5m6CT4-Jsx5dNHYYcLJ-G7VU6TuCildBXlWqpNXzxI97cNuOttOb4EYMf_T-GKn_ad_HmK7QB5yMiy9YIVjBKUvYlx1mgo8x2F4bNycb_DQHdIMGqp8t0v9apIHpIiWZ9PI__d8NryvzndLF2f5-kWF40EIyWerrn_f6_Ire3d9dnusm8Sc7vkevcZ1s1LerggKjRSXKkgF7Au-mspo |
| CODEN | COABER |
| CitedBy_id | crossref_primary_10_1155_2015_904541 crossref_primary_10_1093_nar_27_1_49 crossref_primary_10_1109_TITB_2007_904632 crossref_primary_10_1101_gr_10_7_939 crossref_primary_10_1109_TITB_2002_1006299 crossref_primary_10_1101_gr_922503 crossref_primary_10_1093_nar_27_1_263 crossref_primary_10_1093_bioinformatics_bti215 |
| ContentType | Journal Article |
| Copyright | 1997 INIST-CNRS |
| Copyright_xml | – notice: 1997 INIST-CNRS |
| DBID | FBQ BSCLL AAYXX CITATION IQODW CGR CUY CVF ECM EIF NPM 7S9 L.6 7X8 |
| DOI | 10.1093/bioinformatics/13.2.137 |
| DatabaseName | AGRIS Istex CrossRef Pascal-Francis Medline MEDLINE MEDLINE (Ovid) MEDLINE MEDLINE PubMed AGRICOLA AGRICOLA - Academic MEDLINE - Academic |
| DatabaseTitle | CrossRef MEDLINE Medline Complete MEDLINE with Full Text PubMed MEDLINE (Ovid) AGRICOLA AGRICOLA - Academic MEDLINE - Academic |
| DatabaseTitleList | MEDLINE AGRICOLA MEDLINE - Academic |
| Database_xml | – sequence: 1 dbid: NPM name: PubMed url: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed sourceTypes: Index Database – sequence: 2 dbid: 7X8 name: MEDLINE - Academic url: https://search.proquest.com/medline sourceTypes: Aggregation Database |
| DeliveryMethod | fulltext_linktorsrc |
| Discipline | Biology |
| EISSN | 1460-2059 |
| EndPage | 143 |
| ExternalDocumentID | 9146960 2632403 10_1093_bioinformatics_13_2_137 ark_67375_HXZ_BG0VZVFB_L US201302865531 |
| Genre | Research Support, Non-U.S. Gov't Journal Article Comparative Study |
| GroupedDBID | -~X .2P .I3 482 48X 53G 5GY AAIMJ AAJKP AAKPC AAMVS AAPQZ AAPXW AARHZ AAVAP ABEFU ABEJV ABGNP ABJNI ABNGD ABNKS ABPTD ABSMQ ABWST ABXVV ABZBJ ACGFS ACPQN ACUFI ACUKT ACYTK ADEYI ADFTL ADGZP ADHKW ADOCK ADRTK ADYVW ADZTZ ADZXQ AECKG AEGPL AEJOX AEKKA AEKPW AEKSI AELWJ AEPUE AETBJ AFFNX AFFZL AFOFC AFSHK AGINJ AGKRT AGQXC AI. ALMA_UNASSIGNED_HOLDINGS ALTZX AQDSO ARIXL ASAOO ATDFG ATTQO AXUDD AYOIW AZFZN AZVOD BHONS CXTWN CZ4 DFGAJ EE~ ELUNK F5P F9B FBQ FEDTE H5~ HAR HVGLF HW0 IOX KSI KSN MBTAY MVM NGC PB- Q1. Q5Y QBD RD5 RIG ROL ROZ RXO TLC TN5 TOX TR2 VH1 WH7 XJT ZGI ~91 AGQPQ BSCLL --- -E4 .-4 .DC .GJ 0R~ 1TH 23N 2WC 4.4 5WA 70D AAIJN AAJQQ AAMDB AAOGV AAUQX AAVLN AAYXX ABEUO ABIXL ABPQP ABQLI ACIWK ACPRK ACUXJ ADBBV ADEZT ADGKP ADHZD ADMLS ADPDF ADRDM ADVEK AEMDU AENEX AENZO AEWNT AFGWE AFIYH AFRAH AGKEF AGSYK AHMBA AHXPO AIJHB AJEEA AJEUX AKHUL AKWXX ALUQC AMNDL APIBT APWMN ASPBG AVWKF BAWUL BAYMD BQDIO BQUQU BSWAC BTQHN C1A C45 CAG CDBKE CITATION COF CS3 DAKXR DIK DILTD DU5 D~K EBD EBS EJD EMOBN FHSFR FLIZI FLUFQ FOEOM FQBLK GAUVT GJXCC GROUPED_DOAJ GX1 H13 HZ~ J21 JXSIZ KAQDR KOP KQ8 M-Z MK~ ML0 N9A NLBLG NMDNZ NOMLY NTWIH NU- NVLIB O0~ O9- OAWHX ODMLO OJQWA OK1 OVD OVEED O~Y P2P PAFKI PEELM PQQKQ R44 RNI RNS RPM RUSNO RW1 RZF RZO SV3 TEORI TJP W8F WOQ X7H YAYTL YKOAZ YXANX ZKX ~KM IQODW 6.Y ADRIX AFXEN BCRHZ CGR CUY CVF ECM EIF NPM ROX TCN 7S9 L.6 7X8 |
| ID | FETCH-LOGICAL-c411t-1ee9bd4e9189695df5df7da3a503c663b8719a81ff8adab690daa6e7c4a1e6993 |
| ISICitedReferencesCount | 55 |
| ISICitedReferencesURI | http://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=Summon&SrcAuth=ProQuest&DestLinkType=CitingArticles&DestApp=WOS_CPL&KeyUT=10.1093/bioinformatics/13.2.137&url=https%3A%2F%2Fcvtisr.summon.serialssolutions.com%2F%23%21%2Fsearch%3Fho%3Df%26include.ft.matches%3Dt%26l%3Dnull%26q%3D |
| ISSN | 0266-7061 1367-4803 |
| IngestDate | Sun Nov 09 13:37:44 EST 2025 Thu Sep 04 16:16:39 EDT 2025 Wed Feb 19 01:14:28 EST 2025 Mon Jul 21 09:17:24 EDT 2025 Tue Nov 18 22:34:18 EST 2025 Sat Nov 29 03:55:43 EST 2025 Sat Sep 20 11:01:47 EDT 2025 Thu Apr 03 09:42:12 EDT 2025 |
| IsDoiOpenAccess | false |
| IsOpenAccess | true |
| IsPeerReviewed | true |
| IsScholarly | true |
| Issue | 2 |
| Keywords | Proteins Nucleotide sequence Computerized processing Database Software Method Algorithm Nucleic acid Comparative study Aminoacid sequence |
| Language | English |
| License | CC BY 4.0 |
| LinkModel | OpenURL |
| MergedId | FETCHMERGED-LOGICAL-c411t-1ee9bd4e9189695df5df7da3a503c663b8719a81ff8adab690daa6e7c4a1e6993 |
| Notes | 1To whom correspondence should be addressed ArticleID:13.2.137 ark:/67375/HXZ-BG0VZVFB-L istex:E0BEE9383E2A7F13C518722075E78B3CEFE9A701 ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 ObjectType-Article-2 ObjectType-Feature-1 |
| OpenAccessLink | https://academic.oup.com/bioinformatics/article-pdf/13/2/137/689405/13-2-137.pdf |
| PMID | 9146960 |
| PQID | 48895089 |
| PQPubID | 24069 |
| PageCount | 7 |
| ParticipantIDs | proquest_miscellaneous_79005606 proquest_miscellaneous_48895089 pubmed_primary_9146960 pascalfrancis_primary_2632403 crossref_citationtrail_10_1093_bioinformatics_13_2_137 crossref_primary_10_1093_bioinformatics_13_2_137 istex_primary_ark_67375_HXZ_BG0VZVFB_L fao_agris_US201302865531 |
| PublicationCentury | 1900 |
| PublicationDate | 1997-04-01 |
| PublicationDateYYYYMMDD | 1997-04-01 |
| PublicationDate_xml | – month: 04 year: 1997 text: 1997-04-01 day: 01 |
| PublicationDecade | 1990 |
| PublicationPlace | Washington, DC Oxford |
| PublicationPlace_xml | – name: Oxford – name: Washington, DC – name: England |
| PublicationTitle | Bioinformatics |
| PublicationTitleAlternate | Comput Appl Biosci |
| PublicationYear | 1997 |
| Publisher | Oxford University Press |
| Publisher_xml | – name: Oxford University Press |
| SSID | ssj0051444 ssj0005056 |
| Score | 1.7473263 |
| Snippet | Motivation: This paper presents LASSAP, a new software package for sequence comparison. LASSAP is a programmable, high-performance system designed to raise... Motivation This paper presents LASSAP, a new software package for sequence comparison. LASSAP is a programmable, high-performance system designed to raise... This paper presents LASSAP, a new software package for sequence comparison. LASSAP is a programmable, high-performance system designed to raise current... |
| SourceID | proquest pubmed pascalfrancis crossref istex fao |
| SourceType | Aggregation Database Index Database Enrichment Source Publisher |
| StartPage | 137 |
| SubjectTerms | algorithm integration Algorithms Amino Acid Sequence amino acid sequences Base Sequence Biological and medical sciences comparisons computer analysis computer software Databases, Factual Evaluation Studies as Topic Fundamental and applied biological sciences. Psychology General aspects genetics Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects) methods Molecular Sequence Data Nucleic Acids Nucleic Acids - genetics nucleotide sequences Proteins Proteins - genetics Sequence Alignment Sequence Alignment - methods Sequence Alignment - statistics & numerical data Software statistics & numerical data |
| Title | LASSAP, a LArge Scale Sequence compArison Package |
| URI | https://api.istex.fr/ark:/67375/HXZ-BG0VZVFB-L/fulltext.pdf https://www.ncbi.nlm.nih.gov/pubmed/9146960 https://www.proquest.com/docview/48895089 https://www.proquest.com/docview/79005606 |
| Volume | 13 |
| WOSCitedRecordID | wos10.1093/bioinformatics/13.2.137&url=https%3A%2F%2Fcvtisr.summon.serialssolutions.com%2F%23%21%2Fsearch%3Fho%3Df%26include.ft.matches%3Dt%26l%3Dnull%26q%3D |
| hasFullText | 1 |
| inHoldings | 1 |
| isFullTextHit | |
| isPrint | |
| journalDatabaseRights | – providerCode: PRVASL databaseName: Oxford Open customDbUrl: eissn: 1460-2059 dateEnd: 99991231 omitProxy: false ssIdentifier: ssj0005056 issn: 0266-7061 databaseCode: TOX dateStart: 19850101 isFulltext: true titleUrlDefault: https://academic.oup.com/journals/ providerName: Oxford University Press – providerCode: PRVASL databaseName: Oxford Open customDbUrl: eissn: 1460-2059 dateEnd: 20220930 omitProxy: false ssIdentifier: ssj0005056 issn: 0266-7061 databaseCode: TOX dateStart: 19850101 isFulltext: true titleUrlDefault: https://academic.oup.com/journals/ providerName: Oxford University Press – providerCode: PRVASL databaseName: Oxford Open customDbUrl: eissn: 1460-2059 dateEnd: 19971231 omitProxy: false ssIdentifier: ssj0051444 issn: 0266-7061 databaseCode: TOX dateStart: 19850101 isFulltext: true titleUrlDefault: https://academic.oup.com/journals/ providerName: Oxford University Press |
| link | http://cvtisr.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwtV1da9swFBVLt0Jfxr5Kva2dH8ZeMreWZVvWYzqWlhG6QNIS-iJkSy6lrROSdKT_vlcfdpKOsO1hYISxI0XoXF9J3KN7EPqsJBaxypNAJ_sKYpiTgjxXSRBFONWyOGFJSyM2Qc_OstGI9Z3w38zICdCqyhYLNvmvUMMzAFsfnf0HuJtG4QHcA-hQAuxQ_hXwvc5g0OkbVma715le6UybQjMGHWnasMg7VnqwL4obsc4GqmUe2quh7ZoNmV-73JdL5uHJrY2139moxvJgw1hauaj2Dxd6ku6wHV2hpFgXBNN3QEObLr3xl2TFLqIV54dt-pbfnLJNWAU9dLlg54YC1cXkMDp8UgeGcnJngGHgwpmVGniSENu9aaHnEU2YdsbDn6N69oX1nxHwbXpec_oYOVrvwVH9_zto2zW5tjZplWIMOxb9sS00Y1bMAKzSqp1s3o6YZcnwFXrp9hN-x9rBa_RMVW_QtlUYfXiLsLWGr77wjS34xhb82hb8pS34zhbeofPu9-G308CpZARFjPE8wEqxXMaK4YylLJElXFQKIpKQFLCezGFLzESGyzITUuQpC6UQqaJFLLBKYXm6i7aqcaX2kK9ISaNMJIzFMmZSiVxiUuKCEpUpEQsPpfX48MKlkNdKJrfcUhkIXx9ijgmPoKAeCpuKE5tF5c9V9gAALq5gDPj5IDIRdn2KmmAPfTGoNE2J6Y3mJ9KEn44u-fFJeHF50T3mPQ_tr8HWVDAiBSHx0KcaRg5eVYfKRKXG9zMO05qWR2abf0GZzqIbph7atfg3jTtjer_pxQe0s_zWPqKt-fRe7aMXxa_59Wx6gFp0lB0Ym34EWj6iTA |
| linkProvider | Oxford University Press |
| openUrl | ctx_ver=Z39.88-2004&ctx_enc=info%3Aofi%2Fenc%3AUTF-8&rfr_id=info%3Asid%2Fsummon.serialssolutions.com&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.atitle=LASSAP%2C+a+LArge+Scale+Sequence+compArison+Package&rft.jtitle=Computer+applications+in+the+biosciences&rft.au=Gl%C3%A9met%2C+E&rft.au=Codani%2C+J+J&rft.date=1997-04-01&rft.issn=0266-7061&rft.volume=13&rft.issue=2&rft.spage=137&rft_id=info:doi/10.1093%2Fbioinformatics%2F13.2.137&rft_id=info%3Apmid%2F9146960&rft.externalDocID=9146960 |
| thumbnail_l | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/lc.gif&issn=0266-7061&client=summon |
| thumbnail_m | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/mc.gif&issn=0266-7061&client=summon |
| thumbnail_s | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/sc.gif&issn=0266-7061&client=summon |