An alignment containing only bacterial homologues, human pepsin A and memapsins 1 and 2, generated by extracting the sequences from the MUSCLE alignment and removing all the gap-only columns, is shown in Fig. 1.
An initial list of protein sequences unlikely to be associated with allergy was generated by extracting all protein sequences from Swiss-Prot with the exception of entries containing text strings 'allergen', 'allergy'atopyory' or derivatives thereof in the annotation [12].
Megaleranthis saniculifolia and R. macranthus were used as outgroups by extracting nucleotide sequences of the five genes/regions from the published plastomes.
A multiple-sequence alignment was generated using MUSCLE software for both extracted sequences and the seven full-length PUN1 sequences from NCBI.
For this case, we will prove that problem (1.1) has at least two nonnegative solutions by extracting a minimizing sequence from the Nehari manifold, and we will obtain a sequence of weak solutions with negative energy by the dual fountain theorem.
Let us start by extracting a longer sequence from the phage genome than could possibly be resolved by a single comparison between two USM coordinates.
We also constructed a new matrix consisting of all three codon positions by extracting genes from 13 sequenced chloroplast genomes of land plants (GenBank numbers: AP002983, AP000423, AJ271079, Z00044, AJ400848, AJ506156, AJ428413, X86563, AB042240, X15901, D17510, AP004638, X04465), aligning them, and hand editing apparent mistakes.
A set of negative example sequences was created by extracting all metazoan sequences without peroxisomal association from the Swiss-Prot section of UniProt (http://www.uniprot.org) in November 2011.
Input sequences were created by extracting 200bp from the EcoGene [ 15] database of E. coli intergenic sequences, representing 'background' positions.
