Derivation of the feedback taps of an LFSR from a sequence fragment

1990 ◽  
Vol 26 (17) ◽  
pp. 1352
Author(s):  
D.H. Green
Keyword(s):  
Sequence Fragment

scholarly journals Ultraviolet Photodissociation of tryptic peptide backbones at 213 nm

2020 ◽  
Author(s):  
Lars Kolbowski ◽  
Adam Belsom ◽  
Juri Rappsilber
Keyword(s):  
Reference Beam ◽  
Aromatic Amino Acids ◽  
Sequence Coverage ◽  
E Coli ◽  
Sequence Fragment ◽  
Ultraviolet Photodissociation ◽  
Fragmentation Behavior ◽  
Excitation Time ◽  
Beam Type ◽  
Supplemental Activation

We analyzed the backbone fragmentation behavior of tryptic peptides of a four protein mixture and of E. coli lysate subjected to Ultraviolet Photodissociation (UVPD) at 213 nm on a commercially available UVPD-equipped tribrid mass spectrometer. We obtained 15,178 high-confidence peptide-spectrum matches by additionally recording a reference beam-type collision-induced dissociation (HCD) spectrum of each precursor. Type a, b and y ions were most prominent in UVPD spectra and median sequence coverage ranged from 5.8% (at 5 ms laser excitation time) to 45.0% (at 100 ms). Overall sequence fragment intensity remained relatively low (median: 0.4% (5 ms) to 16.8% (100 ms) of total intensity) and remaining precursor intensity high. Sequence coverage and sequence fragment intensity ratio correlated with precursor charge density, suggesting that UVPD at 213 nm may suffer from newly formed fragments sticking together due to non-covalent interactions. UVPD fragmentation efficiency therefore might benefit from supplemental activation, as was shown for ETD. Aromatic amino acids, most prominently tryptophan, facilitated UVPD. This points at aromatic tags as possible enhancers of UVPD. Data are available via ProteomeXchange with identifier PXD018176 and on spectrumviewer.org/db/UVPD_213nm_trypPep.

scholarly journals ISQuest: finding insertion sequences in prokaryotic sequence fragment data

2015 ◽  
Vol 31 (21) ◽  
pp. 3406-3412 ◽  
Author(s):  
Abhishek Biswas ◽  
David T. Gauthier ◽  
Desh Ranjan ◽  
Mohammad Zubair
Keyword(s):  
Insertion Sequences ◽  
Sequence Fragment

scholarly journals Tephrosia purpurea Represents a New Host of 16SrII-V Subgroup Phytoplasma Associated with Witches’-Broom Disease in China

Plant Disease ◽  
2021 ◽  
Author(s):  
Shao-shuai Yu ◽  
Rui-ling Zhao ◽  
Ming-xing Lin ◽  
Yuan Wu ◽  
Wei wei Song ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Sequence Fragment ◽  
Tephrosia Purpurea ◽  
Seca Gene ◽  
The 16S Rrna Gene

Tephrosia purpurea is a medical plant with excellent insecticidal activity belonging to the family of Leguminosae distributed throughout southern of China (Pei et al., 2013). During January to February 2021, the plants showing abnormal symptoms including witches’-broom, internode shortening, leaf chlorosis and leaflet formation, as shown in Fig.1, were found in Ledong County of Hainan Province, a tropical island in China, with about 60 % incidence. The Tephrosia purpurea disease symptoms were suspected to be induced by phytoplasma, a phloem-limited prokaryotic pathogen which can not be cultured in vitro and which causes severe financial loss and ecological damage to the island. Total DNA from the symptomatic and asymptomatic samples of Tephrosia purpurea were extracted using 0.10 g fresh plant leaves and branches by CTAB method (Doyle and Doyle, 1990). 16S rRNA and secA gene sequence fragments of phytoplasma were detected through PCR amplification using primers R16mF2/R16mR1 (Gundersen and Lee, 1996) and secAfor1/secArev3 (Hodgetts et al., 2008). The two gene sequence fragments of phytoplasma were obtained from the DNA of six symptomatic plant samples whereas not from the DNA of six asymptomatic plant samples. These amplified products were sequenced and the data were deposited in GenBank. The two gene sequence fragments of the DNA obtained from the diseased plant samples were all identical, with a length of 1335 bp for the 16S rRNA (GenBank accession: MW616560) and 729 bp for the secA gene (MW603929). The secA gene fragment putatively encodes for 242 amino acids. The phytoplasma strain was named as Tephrosia purpurea witches’-broom (TpWB) phytoplasma, TpWB-hnld strain. 16S rRNA gene sequence fragment of TpWB-hnld was analyzed by online tool iPhyClassifier (Wei et al., 2007), indicating that the pathogen strain was a member of subgroup 16SrII-V and a ‘Candidatus Phytoplasma aurantifolia’-related strain. Blast analysis based on the 16S rRNA gene sequence fragment of TpWB-hnld showed 100 % sequence identity with that of peanut witches’-broom group members (16SrII group), such as Cassava witches'-broom phytoplasma (KM280679) and Cleome sp. phytoplasma (KM280677); Blast analysis based on the secA gene sequence fragment of TpWB-hnld showed 100 % sequence identity with that of peanut witches’-broom group members (16SrII group), such as sesame phyllody phytoplasma (JN977044). Homology and phylogeny were analyzed using the software of DNAMAN 5.0 and MEGA 7.0, indicating that TpWB-hnld and other subgroup 16SrII-V phytoplasma strains, including Cassava witches'-broom phytoplasma, Cleome sp. phytoplasma, Crotalaria witches'-broom phytoplasma (EU650181) and Desmodium ovalifolium witches'-broom phytoplasma (GU113152), were clustered into one clade with 98 % bootstrap value based on the 16S rRNA gene sequence fragments; TpWB-hnld and sesame phyllody phytoplasma were clustered into one clade based on the secA gene sequence fragments. Multiple alignment based on the 16S rRNA gene sequence fragment showed that the TpWB-hnld phytoplasma strain showed 98 % sequence identity with TpWB phytoplasma strain (HG792252) belonging to 16SrII-M subgroup reported in India (Yadav et al., 2014). To our knowledge, this was the first time that 16SrII-V subgroup phytoplasma associated with Tephrosia purpurea witches’-broom disease was identified in China. Molecular analysis based on the 16S rRNA and secA gene sequence fragments indicated that TpWB-hnld phytoplasma was a member of subgroup 16SrII-V and a ‘Candidatus Phytoplasma aurantifolia’-related strain.

scholarly journals Characterizing circular peptides in mixtures: sequence fragment assembly of cyclotides from a violet plant by MALDI-TOF/TOF mass spectrometry

Amino Acids ◽  
2012 ◽  
Vol 44 (2) ◽  
pp. 581-595 ◽  
Author(s):  
Hossein Hashempour ◽  
Johannes Koehbach ◽  
Norelle L. Daly ◽  
Alireza Ghassempour ◽  
Christian W. Gruber
Keyword(s):  
Mass Spectrometry ◽  
Fragment Assembly ◽  
Sequence Fragment ◽  
Maldi Tof
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