SEQEL: a tool for biological sequence manipulation in Emacs
Summary Sequences are arguably the most common biological data. An easy-to-use tool can greatly facilitate daily manipulation and analysis of biological sequences. Here, we present SEQEL, a tool providing a convenient environment for editing, formatting and rendering of DNA, RNA and protein sequence...
Saved in:
Published in | Bioinformatics Advances Vol. 1; no. 1; p. vbab019 |
---|---|
Main Authors | , |
Format | Journal Article |
Language | English |
Published |
England
Oxford University Press
2021
|
Subjects | |
Online Access | Get full text |
Cover
Loading…
Abstract | Summary
Sequences are arguably the most common biological data. An easy-to-use tool can greatly facilitate daily manipulation and analysis of biological sequences. Here, we present SEQEL, a tool providing a convenient environment for editing, formatting and rendering of DNA, RNA and protein sequences. This is accomplished by extending the commonly used text editor, Emacs, which is available for Windows, Linux and Mac OS.
Availability and Implementation
The unit tested ELISP source code for seqel is freely available from https://github.com/rnaer/seqel along with documentation.
Contact
zhenjiang.xu@gmail.com |
---|---|
AbstractList | Summary Sequences are arguably the most common biological data. An easy-to-use tool can greatly facilitate daily manipulation and analysis of biological sequences. Here, we present SEQEL, a tool providing a convenient environment for editing, formatting and rendering of DNA, RNA and protein sequences. This is accomplished by extending the commonly used text editor, Emacs, which is available for Windows, Linux and Mac OS. Availability and Implementation The unit tested ELISP source code for seqel is freely available from https://github.com/rnaer/seqel along with documentation. Contact zhenjiang.xu@gmail.com Summary Sequences are arguably the most common biological data. An easy-to-use tool can greatly facilitate daily manipulation and analysis of biological sequences. Here, we present SEQEL, a tool providing a convenient environment for editing, formatting and rendering of DNA, RNA and protein sequences. This is accomplished by extending the commonly used text editor, Emacs, which is available for Windows, Linux and Mac OS. Availability and Implementation The unit tested ELISP source code for seqel is freely available from https://github.com/rnaer/seqel along with documentation. Contact zhenjiang.xu@gmail.com Sequences are arguably the most common biological data. An easy-to-use tool can greatly facilitate daily manipulation and analysis of biological sequences. Here, we present SEQEL, a tool providing a convenient environment for editing, formatting and rendering of DNA, RNA and protein sequences. This is accomplished by extending the commonly used text editor, Emacs, which is available for Windows, Linux and Mac OS. The unit tested ELISP source code for seqel is freely available from https://github.com/rnaer/seqel along with documentation. zhenjiang.xu@gmail.com. Sequences are arguably the most common biological data. An easy-to-use tool can greatly facilitate daily manipulation and analysis of biological sequences. Here, we present SEQEL, a tool providing a convenient environment for editing, formatting and rendering of DNA, RNA and protein sequences. This is accomplished by extending the commonly used text editor, Emacs, which is available for Windows, Linux and Mac OS.SummarySequences are arguably the most common biological data. An easy-to-use tool can greatly facilitate daily manipulation and analysis of biological sequences. Here, we present SEQEL, a tool providing a convenient environment for editing, formatting and rendering of DNA, RNA and protein sequences. This is accomplished by extending the commonly used text editor, Emacs, which is available for Windows, Linux and Mac OS.The unit tested ELISP source code for seqel is freely available from https://github.com/rnaer/seqel along with documentation.Availability and ImplementationThe unit tested ELISP source code for seqel is freely available from https://github.com/rnaer/seqel along with documentation.zhenjiang.xu@gmail.com.Contactzhenjiang.xu@gmail.com. |
Author | Xu, Zhenjiang Zech Lu, Hui |
AuthorAffiliation | State Key Laboratory of Food Science and Technology, Nanchang University , Nanchang, Jiangxi 330029, China |
AuthorAffiliation_xml | – name: State Key Laboratory of Food Science and Technology, Nanchang University , Nanchang, Jiangxi 330029, China |
Author_xml | – sequence: 1 givenname: Zhenjiang Zech surname: Xu fullname: Xu, Zhenjiang Zech email: zhenjiang.xu@gmail.com organization: State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, Jiangxi 330029, China – sequence: 2 givenname: Hui orcidid: 0000-0003-1054-5867 surname: Lu fullname: Lu, Hui organization: State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, Jiangxi 330029, China |
BackLink | https://www.ncbi.nlm.nih.gov/pubmed/36700085$$D View this record in MEDLINE/PubMed |
BookMark | eNqFkc1LJDEQxYOM6Khz9bg07MU9tOarO51dWJBhVoUBEfUcqtOJZuhOZjvdA_vfb2RGUS-eiqJ-9XhV7whNfPAGoVOCzwmW7KJ2AZrNxaaGGhO5h6a0ZEWOMScTNCWsFDmvMDtEsxhXGGMqREk4O0CHaZT6qpiiX_eLu8XyZwbZEEKb2dBnSbUNT05Dm0XzdzRem6wD79ZjC4MLPnM-W3Sg4wnat9BGM9vVY_T4Z_Ewv86Xt1c388tlrjkWQ06tlRYqoEVDMeOysJRDiYmFEoxhDac1F42QJW0EJTVobBtcCKhqzaUtKTtGv7e667HuTKONH3po1bp3HfT_VACnPk68e1ZPYaOkIElIJIGznUAf0kFxUJ2L2rQteBPGqKgopZSsYkVCv39CV2HsfTpPMSLTTxkVL46-vXf0ZuX1rwk43wK6DzH2xr4hBKuX7NQ2O7XLLi382C6Ecf0V-x_NjZtd |
Cites_doi | 10.1093/nar/gkh410 10.1093/bioinformatics/btu531 10.1016/j.sbi.2006.04.004 10.1016/j.cell.2019.07.016 10.1038/s41587-019-0209-9 10.1136/gutjnl-2017-314281 10.1093/bioinformatics/bth489 10.1038/nrg3367 10.1093/bioinformatics/bty126 10.2144/00286ir01 10.1042/bj0490481 |
ContentType | Journal Article |
Copyright | The Author(s) 2021. Published by Oxford University Press. 2021 The Author(s) 2021. Published by Oxford University Press. The Author(s) 2021. Published by Oxford University Press. This work is published under http://creativecommons.org/licenses/by/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License. |
Copyright_xml | – notice: The Author(s) 2021. Published by Oxford University Press. 2021 – notice: The Author(s) 2021. Published by Oxford University Press. – notice: The Author(s) 2021. Published by Oxford University Press. This work is published under http://creativecommons.org/licenses/by/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License. |
DBID | TOX AAYXX CITATION NPM 7X8 5PM |
DOI | 10.1093/bioadv/vbab019 |
DatabaseName | Oxford Journals Open Access Collection CrossRef PubMed MEDLINE - Academic PubMed Central (Full Participant titles) |
DatabaseTitle | CrossRef PubMed MEDLINE - Academic |
DatabaseTitleList | PubMed MEDLINE - Academic |
Database_xml | – sequence: 1 dbid: NPM name: PubMed url: https://proxy.k.utb.cz/login?url=http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed sourceTypes: Index Database – sequence: 2 dbid: TOX name: Oxford Journals Open Access Collection url: https://academic.oup.com/journals/ sourceTypes: Publisher |
DeliveryMethod | fulltext_linktorsrc |
Discipline | Biology |
EISSN | 2635-0041 |
ExternalDocumentID | PMC9710577 36700085 10_1093_bioadv_vbab019 10.1093/bioadv/vbab019 |
Genre | Journal Article Report |
GrantInformation_xml | – fundername: ; grantid: 31970088 – fundername: ; grantid: 20192BBF60026 |
GroupedDBID | --- -E4 -~X .-4 .2P .DC .GJ .I3 0R~ 1TH 23N 2WC 4.4 48X 53G 5GY 5WA 70D AAIJN AAIMJ AAJKP AAJQQ AAKPC AAMDB AAMVS AAOGV AAPQZ AAPXW AAUQX AAVAP AAVLN ABEFU ABEJV ABEUO ABIXL ABNGD ABNKS ABPTD ABQLI ABQTQ ABWST ABXVV ABZBJ ACGFS ACIWK ACMRT ACPRK ACUFI ACYTK ADBBV ADEYI ADEZT ADFTL ADGKP ADGZP ADHKW ADHZD ADOCK ADPDF ADRDM ADRIX ADRTK ADVEK ADYVW ADZTZ ADZXQ AECKG AEGPL AEJOX AEKKA AEKSI AELWJ AEMDU AENEX AENZO AEPUE AETBJ AEWNT AFFNX AFFZL AFGWE AFIYH AFOFC AFRAH AFXEN AGINJ AGKEF AGQXC AGSYK AHMBA AHXPO AI. AIJHB AJEEA AJEUX AKHUL AKWXX ALMA_UNASSIGNED_HOLDINGS ALTZX ALUQC AMNDL APIBT APWMN AQDSO ARIXL ASPBG ATTQO AVWKF AXUDD AYOIW AZFZN AZVOD BAWUL BAYMD BCRHZ BHONS BQDIO BQUQU BSWAC BTQHN C1A C45 CAG CDBKE COF CS3 CZ4 DAKXR DIK DILTD DU5 D~K EBD EBS EE~ EJD ELUNK EMOBN F5P F9B FEDTE FHSFR FLIZI FLUFQ FOEOM FQBLK GAUVT GJXCC GROUPED_DOAJ GX1 H13 H5~ HAR HVGLF HW0 HZ~ IOX J21 JXSIZ KAQDR KOP KQ8 KSI KSN M-Z M49 MK~ ML0 N9A NGC NLBLG NMDNZ NOMLY NTWIH NU- NVLIB O0~ O9- OAWHX ODMLO OJQWA OK1 OVD OVEED O~Y P2P PAFKI PB- PEELM PQQKQ Q1. Q5Y R44 RD5 RIG RNI RNS ROL ROX RPM RUSNO RW1 RXO RZF RZO SV3 TEORI TJP TLC TOX TR2 VH1 W8F WOQ X7H XJT YAYTL YKOAZ YXANX ZGI ZKX ~91 ~KM AAYXX ABGNP BBNVY CITATION HCIFZ M~E ZCN ABDBF NPM 7X8 5PM |
ID | FETCH-LOGICAL-c407t-2ff9fa8a25d203495f24a601fa6aee3d42b47d7962d721bac0fd057a8bc49f623 |
IEDL.DBID | TOX |
ISSN | 1367-4803 2635-0041 |
IngestDate | Thu Aug 21 18:38:08 EDT 2025 Fri Jul 11 12:42:14 EDT 2025 Fri Jul 25 12:02:28 EDT 2025 Wed Feb 19 02:25:48 EST 2025 Tue Jul 01 01:54:12 EDT 2025 Wed Jan 22 08:16:47 EST 2025 |
IsDoiOpenAccess | true |
IsOpenAccess | true |
IsPeerReviewed | true |
IsScholarly | true |
Issue | 1 |
Language | English |
License | This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. https://creativecommons.org/licenses/by/4.0 The Author(s) 2021. Published by Oxford University Press. |
LinkModel | DirectLink |
MergedId | FETCHMERGED-LOGICAL-c407t-2ff9fa8a25d203495f24a601fa6aee3d42b47d7962d721bac0fd057a8bc49f623 |
Notes | SourceType-Scholarly Journals-1 content type line 14 ObjectType-Report-1 ObjectType-Article-1 ObjectType-Feature-2 content type line 23 The authors wish it to be known that, in their opinion, the first two authors should be regarded as Joint Authors. |
ORCID | 0000-0003-1054-5867 |
OpenAccessLink | https://dx.doi.org/10.1093/bioadv/vbab019 |
PMID | 36700085 |
PQID | 3191363272 |
PQPubID | 7215308 |
ParticipantIDs | pubmedcentral_primary_oai_pubmedcentral_nih_gov_9710577 proquest_miscellaneous_2769993835 proquest_journals_3191363272 pubmed_primary_36700085 crossref_primary_10_1093_bioadv_vbab019 oup_primary_10_1093_bioadv_vbab019 |
ProviderPackageCode | CITATION AAYXX |
PublicationCentury | 2000 |
PublicationDate | 2021-00-00 |
PublicationDateYYYYMMDD | 2021-01-01 |
PublicationDate_xml | – year: 2021 text: 2021-00-00 |
PublicationDecade | 2020 |
PublicationPlace | England |
PublicationPlace_xml | – name: England – name: Oxford |
PublicationTitle | Bioinformatics Advances |
PublicationTitleAlternate | Bioinform Adv |
PublicationYear | 2021 |
Publisher | Oxford University Press |
Publisher_xml | – name: Oxford University Press |
References | Coker (2022111617292094600_vbab019-B3) 2018; 67 Sberro (2022111617292094600_vbab019-B10) 2019; 178 Griffiths-Jones (2022111617292094600_vbab019-B6) 2005; 21 Sun (2022111617292094600_vbab019-B12) 2018; 34 Amnon (2022111617292094600_vbab019-B1) 2017; 2 Dong (2022111617292094600_vbab019-B4) 2004; 32 Larsson (2022111617292094600_vbab019-B7) 2014; 30 Bolyen (2022111617292094600_vbab019-B2) 2019; 37 Nagarajan (2022111617292094600_vbab019-B8) 2013; 14 Stothard (2022111617292094600_vbab019-B11) 2000; 28 Sanger (2022111617292094600_vbab019-B9) 1951; 49 Edgar (2022111617292094600_vbab019-B5) 2006; 16 |
References_xml | – volume: 32 start-page: W660 year: 2004 ident: 2022111617292094600_vbab019-B4 article-title: PlasMapper: a web server for drawing and auto-annotating plasmid maps publication-title: Nucleic Acids Res doi: 10.1093/nar/gkh410 – volume: 30 start-page: 3276 year: 2014 ident: 2022111617292094600_vbab019-B7 article-title: AliView: a fast and lightweight alignment viewer and editor for large datasets publication-title: Bioinformatics doi: 10.1093/bioinformatics/btu531 – volume: 2 start-page: e00191 year: 2017 ident: 2022111617292094600_vbab019-B1 article-title: Deblur rapidly resolves single-nucleotide community sequence patterns publication-title: mSystems – volume: 16 start-page: 368 year: 2006 ident: 2022111617292094600_vbab019-B5 article-title: Multiple sequence alignment publication-title: Curr. Opin. Struct. Biol doi: 10.1016/j.sbi.2006.04.004 – volume: 178 start-page: 1245 year: 2019 ident: 2022111617292094600_vbab019-B10 article-title: Large-scale analyses of human microbiomes reveal thousands of small, novel genes publication-title: Cell doi: 10.1016/j.cell.2019.07.016 – volume: 37 start-page: 852 year: 2019 ident: 2022111617292094600_vbab019-B2 article-title: Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2 publication-title: Nat. Biotechnol doi: 10.1038/s41587-019-0209-9 – volume: 67 start-page: 1024 year: 2018 ident: 2022111617292094600_vbab019-B3 article-title: Mucosal microbiome dysbiosis in gastric carcinogenesis publication-title: Gut doi: 10.1136/gutjnl-2017-314281 – volume: 21 start-page: 257 year: 2005 ident: 2022111617292094600_vbab019-B6 article-title: RALEE–RNA ALignment editor in Emacs publication-title: Bioinformatics doi: 10.1093/bioinformatics/bth489 – volume: 14 start-page: 157 year: 2013 ident: 2022111617292094600_vbab019-B8 article-title: Sequence assembly demystified publication-title: Nat. Rev. Genet doi: 10.1038/nrg3367 – volume: 34 start-page: 2493 year: 2018 ident: 2022111617292094600_vbab019-B12 article-title: FasParser2: a graphical platform for batch manipulation of tremendous amount of sequence data publication-title: Bioinformatics doi: 10.1093/bioinformatics/bty126 – volume: 28 start-page: 1102 year: 2000 ident: 2022111617292094600_vbab019-B11 article-title: The sequence manipulation suite: JavaScript programs for analyzing and formatting protein and DNA sequences publication-title: Biotechniques doi: 10.2144/00286ir01 – volume: 49 start-page: 481 year: 1951 ident: 2022111617292094600_vbab019-B9 article-title: The amino-acid sequence in the phenylalanyl chain of insulin. 2. The investigation of peptides from enzymic hydrolysates publication-title: Biochem. J doi: 10.1042/bj0490481 |
SSID | ssj0002776143 ssj0005056 |
Score | 2.3464878 |
Snippet | Summary
Sequences are arguably the most common biological data. An easy-to-use tool can greatly facilitate daily manipulation and analysis of biological... Sequences are arguably the most common biological data. An easy-to-use tool can greatly facilitate daily manipulation and analysis of biological sequences.... Summary Sequences are arguably the most common biological data. An easy-to-use tool can greatly facilitate daily manipulation and analysis of biological... |
SourceID | pubmedcentral proquest pubmed crossref oup |
SourceType | Open Access Repository Aggregation Database Index Database Publisher |
StartPage | vbab019 |
SubjectTerms | Application Note Nucleotide sequence |
Title | SEQEL: a tool for biological sequence manipulation in Emacs |
URI | https://www.ncbi.nlm.nih.gov/pubmed/36700085 https://www.proquest.com/docview/3191363272 https://www.proquest.com/docview/2769993835 https://pubmed.ncbi.nlm.nih.gov/PMC9710577 |
Volume | 1 |
hasFullText | 1 |
inHoldings | 1 |
isFullTextHit | |
isPrint | |
link | http://utb.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwjV1dS8MwFA0yEHwRv63OEUXwqWxL06bRJ5EOET8QN9hbSZoEB9qK6wb-e2_arq5D0OeENtyb5J6T3JyL0LnSfQ7Al7sauIVLfclcrohxtZUqkVQbU0hsPDwGtyN6N_bHlVj09JcrfO515SQTat6dSyF7hcAnRGCrkj98GtenKYQBHac_e7CN6-WLKxhA2PNqucbVzzXCUeOJ2xLSXE2YXIpAgy20WUFHfF36ehut6XQHrZfFJL920dVL9BzdX2KB8yx7wwBGcamwZN2AFynT2OpdLGp24UmKo3eRTPfQaBANb27dqjSCmwADy11iDDciFMRXxCrM-IZQAdzKiEBo7SlKJGWK8YAooHhSJD2jAJmJUCaUG4A8-6iVZqk-RNhiKhMqz7DEo0KykKqQGVj5LEg46SsHXSwsFH-UChhxeXPtxaUt48qWDjoDA_7Zqb2wb1wtl2kM-wC4yiOMOOi0boaJbm8vRKqz2TQmLAAwC4Tad9BB6Y76V1aFzoJHB7GGo-oOVkS72ZJOXgsxbc5spWN29J-xH6MNYlNaihOYNmrlnzN9Apgkl52Cy3eKw6JOMTW_AQmv39Q |
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=SEQEL%3A+a+tool+for+biological+sequence+manipulation+in+Emacs&rft.jtitle=Bioinformatics+advances&rft.au=Zhenjiang+Zech+Xu&rft.au=Lu%2C+Hui&rft.date=2021&rft.pub=Oxford+University+Press&rft.eissn=2635-0041&rft.volume=1&rft.issue=1&rft_id=info:doi/10.1093%2Fbioadv%2Fvbab019&rft.externalDBID=NO_FULL_TEXT |
thumbnail_l | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/lc.gif&issn=1367-4803&client=summon |
thumbnail_m | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/mc.gif&issn=1367-4803&client=summon |
thumbnail_s | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/sc.gif&issn=1367-4803&client=summon |