BLASTP

[…] ). an initial 23,414 gene models were identified in du054 and 22,573 in wa94.26. of these, 14,735 pairs of predicted gene models appear to be orthologous between the two genomes (reciprocal best-hit blastp, e value ≤ 1e-5). as a preliminary verification of these gene model builds, we identified orthologous counterparts to eight available phytophthora genomes with annotations [ p. infestans , p. […]

[…] gap/missing treat)., functional analyses were conducted on synechococcus by using kegg database v54 []. proteins in synechococcus were aligned against the protein sequences in kegg database by using blastp [] (e-value < 1.0e-10). the best hit of the query was assigned based on the e-value. for multiple best hits with the same e-value, alignment with the best sequence similarity was selected. […]

[…] thirty-five of the apc_jm3.2 orfs are predicted on the forward strand, while the remaining 22 orfs have a reverse orientation. forty-three orfs of apc_jm3.2 were assigned putative functions by blastp, while 11 of the remaining 14 orfs not assigned a blastp function were assigned a putative function by the uniprot database., the identification of an integrase on the genome of phage […]

[…] to use in subsequent multiple sequence alignments. the first criterion was to find homologs which shared greater than 70% of the queried coverage in their amino acid sequences as listed in a blastp search of the ncbi protein sequence database (http://blast.ncbi.nlm.nih.gov/blast.cgi). for the second criterion, we ensured that the searched homologs contained at least one catalytic or cell […]

[…] were auto-annotated using glimmer () and genemark () and refined by manual inspection; the number of protein-coding genes ranges from 76 to 81 (). functions were assigned using phamerator (), blastp (), and hhpred (). no trnas are present in any of the genomes., ssdna, single-stranded dna., all four phages have features of temperate phages, including a tyrosine integrase, an immunity […]

[…] the basic local alignment search tool (blast) from the national center for biotechnology information (ncbi) (). blast searches were conducted at the amino acid level using the protein-protein blast (blastp) function to query nonredundant protein sequences., maximum-likelihood cladograms of 50 known calicivirus vp1 amino acid sequences and 51 known calicivirus s domain amino acid sequences […]

[…] accomplished using the consed software package. complete closed replicons were automatically annotated by the genome annotation system gendb and manually curated. genes were annotated using the best blastp hit at the national center for biotechnology information (ncbi) database (http://www.ncbi.nlm.nih.gov/). replicon sequences were submitted to genbank and registered under bioproject id […]

[…] and laaidl2). these genes encode proteins with two striking features: (1) laaidl1 contains two tandem deaminase domains (fig. ), which resembles the structure of human apobec3b/d/f/g; and (2) in blastp searches using laaidl1 and laaidl2 as queries, avian and primate apobec1 and apobec3g proteins were amongst the top matches (tables  and ). as in sea urchins, laaidl1 and laaidl2 transcripts […]

[…] in were visualized additionally on a leica sp5 microscope using the same laser settings and detection filters as above., the isip1 protein sequence (phatr3_j55031) was used as the seed sequence for blastp analysis against a curated library comprising all protein sequences in uniref, the mmetsp (), and all additional sequences hosted on the jgi portal. this composite database, described […]

[…] version 3.7.1) for illumina-derived reads and then manually curated to close the gaps. putative open reading frames (orfs) were identified by rast version 2.0 and manually curated when necessary. blastp analyses of the putative orfs against the ncbi non-redundant proteins (nr) database, pfam, and interpro scan were used to assess their putative functions by identification of structural […]