The modular, noncontiguous architecture of the antigen receptor genes necessitates their assembly through V(D J recombination.
Datasets of predicted proteins produced by the sequencing consortia often miss homologs, and predicted proteins contain mispredicted exons and introns in many cases, necessitating manual assembly and annotation.
In the absence of a reference, construction of a genome sequence necessitates de novo assembly which may be beyond the ability of many labs due to the large volumes of raw sequence data and extensive bioinformatics required.
This would necessitate a subsequent assembly of the alignments.
Contiguous with the endoplasmic reticulum, the NE separates gene expression (transcription, mRNA maturation) from protein synthesis (translation, folding, assembly), but necessitates a channel for bidirectional trafficking (the nuclear pore complex (NPC)), a mechanism of mechanical support (lamins) and of chromosomal positioning and segregation.
This is partly due to the intrinsic variability of E.coli genomic content, which made it impossible to rely on reference-based assembly and necessitated the use of de novo assembly methods, and also because of the relatively error prone nature of the technology.
The prevalence of sequence errors among existing Ambystoma assemblies necessitated development of a quality-controlled manual editing methodology to minimize error rates within AESTdb contig sequences.
The assembly of proteins necessitates the precise combination of specific amino acids in a highly ordered and controlled manner; this in turn involves the copying, or transcription, into RNA of specific parts of DNA (see below The synthesis of macromolecules: Nucleic acids and proteins).
Highly polyploid species are particularly challenging for assembly and may necessitate specifically tailored assembly pipelines (Schatz et al. 2012).
Furthermore, the lack of reference genome/transcriptome for read mapping generally necessitates the use of self-assemblies of the transcriptomes.
Both BAC clones had areas of reduced quality reads with low or no sequence coverage bordered by regions of low complexity sequence repeats, which necessitated manual curation of the sequence assembly resulting in substantially improved sequence assemblies of two (PGB02) and one (PGB04) contigs.
