Systematic prediction of functionally linked genes in bacterial and archaeal genomes (Record no. 52118)
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| fixed length control field | 02211nam a2200253Ia 4500 |
| 003 - CONTROL NUMBER IDENTIFIER | |
| control field | MX-MdCICY |
| 005 - DATE AND TIME OF LATEST TRANSACTION | |
| control field | 20250625160220.0 |
| 040 ## - CATALOGING SOURCE | |
| Transcribing agency | CICY |
| 090 ## - LOCALLY ASSIGNED LC-TYPE CALL NUMBER (OCLC); LOCAL CALL NUMBER (RLIN) | |
| Classification number (OCLC) (R) ; Classification number, CALL (RLIN) (NR) | B-17958 |
| 008 - FIXED-LENGTH DATA ELEMENTS--GENERAL INFORMATION | |
| fixed length control field | 250602s9999 xx |||||s2 |||| ||und|d |
| 245 10 - TITLE STATEMENT | |
| Title | Systematic prediction of functionally linked genes in bacterial and archaeal genomes |
| 490 0# - SERIES STATEMENT | |
| Volume/sequential designation | Nature Protocols, 14(10), p.3013-3031, 2019 |
| 520 3# - SUMMARY, ETC. | |
| Summary, etc. | Functionally linked genes in bacterial and archaeal genomes are often organized into operons. However, the composition and architecture of operons are highly variable and frequently differ even among closely related genomes. Therefore, to efficiently extract reliable functional predictions for uncharacterized genes from comparative analyses of the rapidly growing genomic databases, dedicated computational approaches are required. We developed a protocol to systematically and automatically identify genes that are likely to be functionally associated with a 'bait' gene or locus by using relevance metrics. Given a set of bait loci and a genomic database defined by the user, this protocol compares the genomic neighborhoods of the baits to identify genes that are likely to be functionally linked to the baits by calculating the abundance of a given gene within and outside the bait neighborhoods and the distance to the bait. We exemplify the performance of the protocol with three test cases, namely, genes linked to CRISPR-Cas systems using the 'CRISPRicity' metric, genes associated with archaeal proviruses and genes linked to Argonaute genes in halobacteria. The protocol can be run by users with basic computational skills. The computational cost depends on the sizes of the genomic dataset and the list of reference loci and can vary from one CPU-hour to hundreds of hours on a supercomputer. |
| 650 14 - SUBJECT ADDED ENTRY--TOPICAL TERM | |
| Topical term or geographic name entry element | BACTERIAL |
| 650 14 - SUBJECT ADDED ENTRY--TOPICAL TERM | |
| Topical term or geographic name entry element | GENOMES |
| 700 12 - ADDED ENTRY--PERSONAL NAME | |
| Personal name | Shmakov, S. A. |
| 700 12 - ADDED ENTRY--PERSONAL NAME | |
| Personal name | Faure, G. |
| 700 12 - ADDED ENTRY--PERSONAL NAME | |
| Personal name | Makarova, K. S. |
| 700 12 - ADDED ENTRY--PERSONAL NAME | |
| Personal name | Wolf, Y. I. |
| 700 12 - ADDED ENTRY--PERSONAL NAME | |
| Personal name | Severinov, K. V. |
| 700 12 - ADDED ENTRY--PERSONAL NAME | |
| Personal name | Koonin, E. V. |
| 856 40 - ELECTRONIC LOCATION AND ACCESS | |
| Uniform Resource Identifier | <a href="https://drive.google.com/file/d/1yD9xH0vfyIJL2CtYT0gRs8vA-mAJeulD/view?usp=drivesdk">https://drive.google.com/file/d/1yD9xH0vfyIJL2CtYT0gRs8vA-mAJeulD/view?usp=drivesdk</a> |
| Public note | Para ver el documento ingresa a Google con tu cuenta: @cicy.edu.mx |
| 942 ## - ADDED ENTRY ELEMENTS (KOHA) | |
| Source of classification or shelving scheme | Clasificación local |
| Koha item type | Documentos solicitados |
| Lost status | Source of classification or shelving scheme | Damaged status | Not for loan | Collection | Home library | Current library | Shelving location | Date acquired | Total checkouts | Full call number | Date last seen | Price effective from | Koha item type |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Clasificación local | Ref1 | CICY | CICY | Documento préstamo interbibliotecario | 25.06.2025 | B-17958 | 25.06.2025 | 25.06.2025 | Documentos solicitados |