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The Salamander Genome Project (SGP) has recently developed and annotated thousands of expressed sequence tags (ESTs) for A. mexicanum and A. t. tigrinum [ 19, 20], generated complete mtDNA sequence for 5 different ambystomatid species [ 21], and completed the first comprehensive genetic linkage map [ 22].
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This article will focus on the description of the methodology followed and the challenges met to develop and annotate the eT database (eTDB).
We have developed, and partially annotated a reference transcript set of over 70,000 sequences for white clover, and used these to identify over 200,000 independent SNPs in approximately 45% of the reference transcript sequences.
With this in mind, we developed, curated and annotated RiceCyc, the metabolic pathway network of rice, and is currently hosted in the Gramene database (http://www.gramene.org/pathway/).org/pathway/
A Human Phenotype Ontology has been developed and used to annotate OMIM entries [ 42], and the broader Mammalian Phenotype Ontology [ 43] is used in both the Mouse and Rat Genome Databases [ 44, 45].
CMM and PY developed the annotation guidelines and annotated the data set used for this study.
Our system achieved an average accuracy of 83.7% when developed and tested on individually annotated genes.
Their system was initially developed and tested on individually annotated genes and later was expanded to all genes in cancer trial documents.
Novel statistical methods have been developed and used to quantitate and annotate the sequence diversity within combinatorial peptide libraries on the basis of small numbers (1 200) of sequences selected at random from commercially available M13 p3-based phage display libraries.
To date, 2156 fingerprints have been developed, manually annotated and deposited in PRINTS.
While we have developed and tested selenoprofiles to annotate eukaryotic selenoproteomes, the strategy that we have employed can be easily ported to prokaryotic genomes as well.
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