bioshell.bioinformatics package

ACorr is a tool for computing various correlations and autocorrelations on time-series. The program reads a file with data observations in a flat format: several columns and many rows. By default it calculates an autocorrelation function for a given column [by default for the first one] for time steps in the range of [0,t_max], where t_max can be specified by option -acorr.tmax. It is also possible to calculate crosscorrelation between two columns or autocorretation of vectors

BBQ reconstructs protein backbone atoms based on CA coordinates

Clust program finds groups of similar objects (cluters) by means of hierarchical clustering algorithm

Hist calculates a 1D od 2D histogram from one-dimensionalor two-dimensional dataApplication reads a file with multiple columns. Then prepares a histogramfrom datafound in a specified column.

Using PRAline (Profile Alignment) tool one can calculate optimaland sub-optimal alignments between two amino acid sequences or sequence profiles. In general, with PRAline one can:

- align two amino acid sequences: use one of the following flags: [-qp -qf -qs] and one of these: [-tp -tf -ts] to provide query and template sequences, respectively

- align two amino acid profiles: use -qb and -tb options to provide input profiles

- align two amino acid sequences (or profiles) with secondary structure information In this case secondary structure must be provided by SEQ files (-qs and -ts options).

PsiBlastSearch - runs PsiBlast program. It is possible to scan a whole range of PsiBlast input prameters. The jobs may be distributed among several threads.

PsiBlastAnalyse - parser and filter for PsiBlast results. The program is intended to parse the results from PriBlastSearch tool, although it can read in any ouput fromBlast or PsiBlast program, providing that is in format "0" (i.e. -m 0 was used to run Blast). This program can read in and combine several blast outfiles. Results may be filtered in several different ways.

RmsCalc is an extremely flexible program for crmsd and drmsd calculations. It can compare a reference structure against one ore more target structures.It is also possible to point RmsCalc to a directory of PDB files. File names may be filtered by a regular expression. The program can calculate crmsd, drmsd, GDT, TM_score and MaxSub scores. These parameters may be evaluated solely on C-alpha atoms, protein backbone or on all atoms that are common for the two structures being compared. It is also possible to compare based on a sequence alignment.

Seqc is a tool for manipulating protein sequences.Seqc reads files in formats: PDB, FASTA, DSSP, SEQ, Blast (sequence profile),and PsiPred (secondary structure prediction output). The informationmay be written in one of the following formats: FASTA and SEQ

StrCalc - simple calculations on protein structures. The program can calculate various distances and angles. It is also possibleto change protein representation into a reduced model basing on a config fileprovided by a user.

Trac is a tool for manipulating files in TRA and PDB formats, containing multiple structures obtained during a simulation. In the case of PDB format, separate structures (frames) are stored as separate MODEL entries (see PDB file format specification for details).

WHAM program reads a file with multiple columns and computes the density of states.

StatPhys calculates various thermodynamic properties as a function of temperature from a density of states and measured observables