MatGAT: An application that generates similarity/identity matrices using protein or DNA sequences
<p>Abstract</p> <p>Background</p> <p>The rapid increase in the amount of protein and DNA sequence information available has become almost overwhelming to researchers. So much information is now accessible that high-quality, functional gene analysis and categorization ha...
| Main Authors: | , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
BMC
2003-07-01
|
| Series: | BMC Bioinformatics |
| Subjects: | |
| Online Access: | http://www.biomedcentral.com/1471-2105/4/29 |
| _version_ | 1819089111096492032 |
|---|---|
| author | Smalley John Bitincka Ledion Campanella James J |
| author_facet | Smalley John Bitincka Ledion Campanella James J |
| author_sort | Smalley John |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>The rapid increase in the amount of protein and DNA sequence information available has become almost overwhelming to researchers. So much information is now accessible that high-quality, functional gene analysis and categorization has become a major goal for many laboratories. To aid in this categorization, there is a need for non-commercial software that is able to both align sequences and also calculate pairwise levels of similarity/identity.</p> <p>Results</p> <p>We have developed MatGAT (Matrix Global Alignment Tool), a simple, easy to use computer application that generates similarity/identity matrices for DNA or protein sequences without needing pre-alignment of the data.</p> <p>Conclusions</p> <p>The advantages of this program over other software are that it is open-source freeware, can analyze a large number of sequences simultaneously, can visualize both sequence alignment and similarity/identity values concurrently, employs global alignment in calculations, and has been formatted to run under both the Unix and the Microsoft Windows Operating Systems. We are presently completing the Macintosh-based version of the program.</p> |
| first_indexed | 2024-12-21T22:02:44Z |
| format | Article |
| id | doaj.art-877fe01193184e238db5c30923c2fdaf |
| institution | Directory Open Access Journal |
| issn | 1471-2105 |
| language | English |
| last_indexed | 2024-12-21T22:02:44Z |
| publishDate | 2003-07-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Bioinformatics |
| spelling | doaj.art-877fe01193184e238db5c30923c2fdaf2022-12-21T18:48:46ZengBMCBMC Bioinformatics1471-21052003-07-01412910.1186/1471-2105-4-29MatGAT: An application that generates similarity/identity matrices using protein or DNA sequencesSmalley JohnBitincka LedionCampanella James J<p>Abstract</p> <p>Background</p> <p>The rapid increase in the amount of protein and DNA sequence information available has become almost overwhelming to researchers. So much information is now accessible that high-quality, functional gene analysis and categorization has become a major goal for many laboratories. To aid in this categorization, there is a need for non-commercial software that is able to both align sequences and also calculate pairwise levels of similarity/identity.</p> <p>Results</p> <p>We have developed MatGAT (Matrix Global Alignment Tool), a simple, easy to use computer application that generates similarity/identity matrices for DNA or protein sequences without needing pre-alignment of the data.</p> <p>Conclusions</p> <p>The advantages of this program over other software are that it is open-source freeware, can analyze a large number of sequences simultaneously, can visualize both sequence alignment and similarity/identity values concurrently, employs global alignment in calculations, and has been formatted to run under both the Unix and the Microsoft Windows Operating Systems. We are presently completing the Macintosh-based version of the program.</p>http://www.biomedcentral.com/1471-2105/4/29nucleic acidproteinsequencealignmentpairwise analysissimilarity matrix |
| spellingShingle | Smalley John Bitincka Ledion Campanella James J MatGAT: An application that generates similarity/identity matrices using protein or DNA sequences BMC Bioinformatics nucleic acid protein sequence alignment pairwise analysis similarity matrix |
| title | MatGAT: An application that generates similarity/identity matrices using protein or DNA sequences |
| title_full | MatGAT: An application that generates similarity/identity matrices using protein or DNA sequences |
| title_fullStr | MatGAT: An application that generates similarity/identity matrices using protein or DNA sequences |
| title_full_unstemmed | MatGAT: An application that generates similarity/identity matrices using protein or DNA sequences |
| title_short | MatGAT: An application that generates similarity/identity matrices using protein or DNA sequences |
| title_sort | matgat an application that generates similarity identity matrices using protein or dna sequences |
| topic | nucleic acid protein sequence alignment pairwise analysis similarity matrix |
| url | http://www.biomedcentral.com/1471-2105/4/29 |
| work_keys_str_mv | AT smalleyjohn matgatanapplicationthatgeneratessimilarityidentitymatricesusingproteinordnasequences AT bitinckaledion matgatanapplicationthatgeneratessimilarityidentitymatricesusingproteinordnasequences AT campanellajamesj matgatanapplicationthatgeneratessimilarityidentitymatricesusingproteinordnasequences |