Ambiguous Nucleotide Tool (ANT), software for generating and evaluating degenerate codons for natural and expanded genetic codes. - mengqvist/ANT

The sequence data must consist of two or more sequences of equal length. All sequences must be aligned (MEGA does not include an alignment program) and should be arranged either in interleaved (block-wise) or in noninterleaved (continuous) format (see below).. Nucleotide or amino acid sequences should be written in IUPAC single-letter codes. In this system, A, T(U), C, and G represent the four different nucleotides, and all alphabets except B, J, O, U, X, and Z represent the twenty different amino acids (see Table 2. 1). However, the use of N (and n) for ambiguous nucleotides and X (and x) for ambiguous amino acid residues must be avoided. Sequences can be written in any combination of upper- and lower-case letters. Special symbols for alignment gaps, missing data, and identical sites can also be included in the sequences. ...

gag p24 transmission clusters of Capetonian sequences.On the right hand side are the two individual gag clusters with their estimated time of origin. On the lef

Other: Comparator: Placebo to the MRKAd5 HIV-1 gag/pol/nef vaccine Biological: Monovalent MRKAd5 HIV-1 gag vaccine (1x10^9 vp/dose) Biological: Trivalent MRKAd5 HIV-1 gag/pol/nef vaccine (3x10^6 vp/dose) Biological: Trivalent MRKAd5 HIV-1 gag/pol/nef vaccine (3x10^7 vp/dose) Biological: Trivalent MRKAd5 HIV-1 gag/pol/nef vaccine (3x10^8 vp/dose) Biological: Trivalent MRKAd5 HIV-1 gag/pol/nef vaccine (3x10^9 vp/dose) Biological: Trivalent MRKAd5 HIV-1 gag/pol/nef vaccine (3x10^10 vp/dose) Biological: Trivalent MRKAd5 HIV-1 gag/pol/nef vaccine (1x10^11 vp/dose) Biological: Comparator: Placebo to MRKAd5 HIV-1 gag vaccine ...

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Molecular characterization of HIV type 1 strains from newly diagnosed patients in Cyprus (2007-2009) recovers multiple clades including unique recombinant strains and lack of transmitted drug resistance ...

Shop Transposon Ty1-DR6 Gag-Pol polyprotein ELISA Kit, Recombinant Protein and Transposon Ty1-DR6 Gag-Pol polyprotein Antibody at MyBioSource. Custom ELISA Kit, Recombinant Protein and Antibody are available.

Shop Transposon Ty1-DR1 Gag-Pol polyprotein ELISA Kit, Recombinant Protein and Transposon Ty1-DR1 Gag-Pol polyprotein Antibody at MyBioSource. Custom ELISA Kit, Recombinant Protein and Antibody are available.

This research will evaluate how high-risk clusters and current prevention strategies affect HIV transmission patterns. There are a number of potential drivers of the epidemic, including substance use, undiagnosed infections and high number of sexual partners. However, it still remains unclear which drivers contribute to the epidemic with HIV transmission as the biological outcome. The study aims to characterize HIV clusters and correlates associated with transmission.

In recent years, multiple circulating recombinant forms (CRFs) and unique recombinant forms of human immunodeficiency virus type 1 (HIV-1) have been described in Yunnan, China. Here, we identified a novel HIV-1 CRF (CRF86_BC) isolated from three heterosexuals with no obvious epidemiologic linkage in western Yunnan (Baoshan prefecture) in China. CRF86_BC had a subtype C backbone with four subtype B fragments inserted into the pol, vpr, vpu, env, and nef gene regions, respectively. Furthermore, subregion tree analysis revealed that subtype C backbone originated from an Indian C lineage and subtype B segment inserted was from a Thai B lineage. They are different from previously documented B/C forms in its distinct backbone, inserted fragment size, and break points. This highlighted the importance of continual monitoring of genetic diversity and complexity of HIV-1 strains in this region.. ...

West-Central Africa is an epicenter of the HIV pandemic; endemic to Cameroon are HIV-1 viruses belonging to all (sub)subtypes and numerous Circulating Recombinant Forms (CRFs). The rural villages of Cameroon harbor many strains of HIV-1, though these areas are not as well monitored as the urban centers. In the present study, 82 specimens obtained in 2000 and 2001 from subjects living in the rural villages of the South and West Regions of Cameroon were subtyped in gag, pol, and env and compared to 90 specimens obtained in 2006-2008 in the same regions, in order to analyze HIV-1 evolution in these rural areas. It was found that in the South Region, the proportion of unique recombinant forms (URFs) remained constant (~40%), while the amount of URFs containing fragments of a CRF increased by 25%. (Sub)subtypes A1, F2, H, and K, and CRF09_cpx, identified in 2000 and 2001, were replaced by CRFs 01_AE, 13_cpx, 14_BG, and 18_cpx in 2006-2008. In the West Region, (sub)subtypes A2, C, G, and H, and CRFs 01_AE and

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RNA-Seq data analysis.The CLC Genomics Workbench version 10.1.1 was used for bioinformatics analyses in this study. RNA-Seq analysis was done by mapping next-generation sequencing reads and distributing and counting the reads across genes and transcripts. The latest assembly of the A. aegypti genome (GCF_000004015.4) was used as a reference. All libraries were trimmed from sequencing primers and adapter sequences. Low-quality reads (quality score below 0.05) and reads with more than 2 ambiguous nucleotides were discarded. Clean reads were subjected to an RNA-Seq analysis toolbox for mapping reads to the reference genome with mismatch, insertion, and deletion costs of 2, 3, and 3, respectively. Mapping was performed with stringent criteria and allowed a length fraction of 0.8 in mapping parameter, in which at least 80% of nucleotides in a read must be aligned to the reference genome. The minimum similarity between the aligned region of the read and the reference sequence was set at ...

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Fellay J, Frahm N, Shianna KV, Cirulli ET, Casimiro DR, Robertson MN, Haynes BF, Geraghty DE, McElrath MJ, Goldstein DB. 2011. Host genetic determinants of T cell responses to the MRKAd5 HIV-1 gag/pol/nef vaccine in the step trial.. The Journal of infectious diseases. 203(6):773-9. Abstract ...

South Africa has the largest worldwide HIV/AIDS population with 5.6 million people infected and at least 2 million people on antiretroviral therapy. The majority of these infections are caused by HIV-1 subtype C. Using genotyping methods we characterized HIV-1 subtypes of the gag p24 and pol PR and RT fragments, from a cohort of female participants in the Western Cape Province, South Africa. These participants were recruited as part of a study to assess the combined brain and behavioural effects of HIV and early childhood trauma. The partial HIV-1 gag and pol fragments of 84 participants were amplified by PCR and sequenced. Different online tools and manual phylogenetic analysis were used for HIV-1 subtyping. Online tools included: REGA HIV Subtyping tool version 3; Recombinant Identification Program (RIP); Context-based Modeling for Expeditious Typing (COMET); jumping profile Hidden Markov Models (jpHMM) webserver; and subtype classification using evolutionary algorithms (SCUEAL). HIV-1 subtype ...

Drug resistance mutations in HIV pol sequences from Argentinean patients under antiretroviral treatment: subtype, gender, and age issues ...

Forty-one HIV-1 strains from Gabonese patients were studied according to the following strategy: nested polymerase chain reaction were performed to obtain an approximately 1,100-bp fragment containing the protease gene and the 5 half of the reverse transcriptase gene. Additional amplifications were carried out to obtain an approximately 700-bp fragment encompassing the C2V3 env gene. Fragments of 600 to 1,200 bp in the gag gene overlapping the pol sequences were used for the study of recombination patterns. Phylogenetic analyses of the different fragments were used to investigate HIV-1 diversity in Gabon. Thirty-one strains were sequenced in the env and pol genes and phylogenetic analyses classified them as subtype A (n = 2), D (n = 4), G (n = 1), H (n = 1), CRF02 (n = 8), and CRF MAL-like (n = 6); in addition, there were 6 unique recombinant forms and 1 unclassified strain, and in 2 cases pol/env sequences classified strains as subtype D whereas gag phylogeny classified them as subtype A. In ...

Gag-Pol polyprotein: Mediates, with Gag polyrotein, the essential events in virion assembly, including binding the plasma membrane, making the protein-protein interactions necessary to create spherical particles, recruiting the viral Env proteins, and packaging the genomic RNA via direct interactions with the RNA packaging sequence (Psi). Gag-Pol polyprotein may regulate its own translation, by the binding genomic RNA in the 5-UTR. At low concentration, the polyprotein would promote translation, whereas at high concentration, the polyprotein would encapsidate genomic RNA and then shutt off translation.